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Monitor the progress of a cloud assembly
Monitor the progress of a cloud assembly
The DNASTAR Cloud Assemblies Web Monitor lets you monitor the progress of your Cloud Assemblies and view text files related to completed assemblies. The Web Monitor is accessible from any device with web access, including computers and mobile devices like tablets and…
Monitor the progress of a Cloud Assembly
Wizard screen descriptions » Run Assembly Project » Monitor the progress of a Cloud Assembly
To monitor the progress of a Cloud Assembly: Once you press the Start Assembly button in the SeqMan NGen wizard, the assembly begins. The Cloud Assembly tutorials in this User Guide each take 30 minutes to several hours to complete. You can monitor the progress using…
SeqMan NGen Tutorials
SeqMan NGen Tutorials
The tutorials listed below all launch from SeqMan Ultra and end with analysis in SeqMan Ultra. The tutorials are available in both this User Guide and the SeqMan Ultra User Guide. Within each tutorial is a link for downloading the corresponding data in archived (.zip)…
Assembly Log
Wizard screen descriptions » Assembly Log
After pressing the Run assembly on this computer link from the Run Assembly screen, the Assembly Log opens to show the status of the assembly. Once the assembly runs to completion without failure, the following text will be displayed: “Assembly finished…
Assembly Options
Wizard screen descriptions » Assembly Options
The Assembly Options wizard screen allows you to specify assembly parameters. This screen comes in several variations, two of which are shown below (click on either to see full-size): Depending on the workflow, only a subset of the…
Assembly Output
Wizard screen descriptions » Assembly Output
When the Assembly Output screen appears in the wizard, you must select a name and location for your project before proceeding further. *Note: If you are setting up a gene homology alignment in MegAlign Pro, click here for information on the specialized version of…
Assembly Summary
Wizard screen descriptions » Assembly Summary
After a local assembly has finished in the Assembly Log, clicking Next > takes you to the Assembly Summary screen. This screen varies based on the data type and workflow. If assembly failed, the dialog displays the message “Assembly failed. No report…
Input Assembly
Wizard screen descriptions » Input Assembly
If you selected Reference-guided scaffolding of existing contigs or Reference-guided scaffolding and contig joining workflow in the Workflow screen, the SeqMan NGen wizard includes a screen called Input Assembly. *Note: This screen is different from the…
Create an assembly for phased variant analysis
Wizard screen descriptions » Workflow » Variant Analysis/Resequencing workflows » Create an assembly for phased variant analysis
The purpose of phased variant analysis is to determine the specific combination of genetic variants (alleles) inherited together on a single chromosome from each parent. Phased variant analysis can be used to: Identify genes that are inherited together (linked)…
Post Assembly Options
Wizard screen descriptions » Post Assembly Options
The Post Assembly Options screen lets you enter a reference sequence against which to order and orient assembled contigs. In some workflows, you can also use this screen to set requirements for minimum contig size. Different subsets of options are available depending…
Run Assembly Project
Wizard screen descriptions » Run Assembly Project
The Run Assembly Project screen follows the Assembly Output screen and prompts you to specify a name for the project and a location in which to save temporary files. You can also review system memory information that will help you make an educated decision whether to…
Cloud Monitor
Wizard screen descriptions » Cloud Monitor
After pressing the Run assembly on the Cloud link in the Run Assembly screen, you will be taken to the Cloud Monitor screen. This is where you monitor in-progress and completed Cloud Assemblies. You can also get to this screen by launching SeqMan NGen and selecting…
Alignment tab (Assembly Options)
Wizard screen descriptions » Options tabs » Alignment tab » Alignment tab (Assembly Options)
The Alignment tab of the Assembly Options dialog is used to set parameters for the alignment phase of the assembly. To access the tab from the Assembly Options screen, click the Advanced Options button then click on the Alignment tab. The options available in this tab…
Trimming tab (Assembly Options)
Wizard screen descriptions » Options tabs » Trimming tab » Trimming tab (Assembly Options)
The Trimming tab of the Assembly Options dialog is used to set parameters for the trimming phase of the assembly. To access the tab from the Assembly Options screen, click the Advanced Options button then click on the Trimming tab. Default parameters vary…
Part A: Running the assembly in SeqMan NGen and viewing it in SeqMan Ultra
SeqMan NGen Tutorials » Long-read analysis with accuracy evaluation » Part A: Running the assembly in SeqMan NGen and viewing it in SeqMan Ultra
In Part A, you will use SeqMan NGen to run the assembly, then launch the results in SeqMan Ultra. Download T5_Long_Read.zip (232 MB) and extract it to any convenient location (i.e., your desktop). Part A of the tutorial will use the files MAP006-1_2D_pass.fastq…
Contents of the .assembly package
Access and understand output files » Reference-guided workflow output » Contents of the .assembly package
The .assembly package is part of the output for XNG workflows. (The contents of the -noSplit.assembly package are similar to those of the .assembly package.) In the file names below, the project name should be understood to precede any hyphen (-) or period (.)…
De novo assembly using Sanger data
SeqMan NGen Tutorials » De novo assembly using Sanger data
In this tutorial, you will de novo assemble fourteen short trace sequences from PE Applied Biosystems, Inc. and then analyze the resulting contig in SeqMan Ultra. Scroll to the bottom of this topic for a short video showing a slightly different version of this tutorial…
Layout tab (Assembly or Analysis Options)
Wizard screen descriptions » Options tabs » Layout tab » Layout tab (Assembly or Analysis Options)
The Layout tab in the Assembly Options and Analysis Options dialogs is used to set parameters for the layout phase of the assembly. To access the tab from the Assembly Options or Analysis Options screens, click the Advanced Options button then click on the Layout tab.…
Log in to Cloud Assemblies
Log in to Cloud Assemblies
To log in to Cloud Assemblies or to access the Cloud Data Drive: If you are not logged into your DNASTAR account and press a button associated with Cloud Assemblies or the Cloud Data Drive (e.g., the Add from Cloud button in the Reference Sequence screen), a popup…
Create a New Cloud Folder
Use the DNASTAR Cloud Data Drive » Create a New Cloud Folder
To create a new folder in the DNASTAR Cloud: Click the Create a new folder on the Cloud tool () and type in a name for the new folder. Press Done; or choose Cancel to exit without creating a folder. If your AWS credentials have not been set up, you will receive…
Troubleshoot issue with scrolling (macOS only)
Appendix » Troubleshoot issue with scrolling (macOS only)
When using Lasergene applications, users of some macOS releases have reported issues when trying to scroll horizontally in application views. No matter which macOS version you use, we highly recommend that you change your system settings to always show scroll bars.…
Close the DNASTAR Cloud Data Drive
Use the DNASTAR Cloud Data Drive » Close the DNASTAR Cloud Data Drive
To close the DNASTAR Cloud Data Drive application: Click Close to exit. or… Click Log out and close to both close the Cloud Data Drive and log off from your DNASTAR account. After using this button, the SeqMan NGen wizard will “forget” your saved…
Use the DNASTAR Cloud Data Drive
Use the DNASTAR Cloud Data Drive
The DNASTAR Cloud Data Drive works as both a Cloud file browser and a mechanism for transferring data between your desktop/laptop computer and the DNASTAR Cloud. Your data and results are stored in a private, encrypted Amazon Web Services (AWS) account visible only to…
Access the DNASTAR Cloud Data Drive
Use the DNASTAR Cloud Data Drive » Access the DNASTAR Cloud Data Drive
Once you have met the license and credential requirements, the Data Drive can be accessed in several ways: Through the SeqMan NGen wizard: In the Welcome screen, select Assemble on the DNASTAR Cloud (currently available on Windows and Macintosh only) if you are…
Part B (optional): Evaluating assembly accuracy using QUAST
SeqMan NGen Tutorials » Long-read analysis with accuracy evaluation » Part B (optional): Evaluating assembly accuracy using QUAST
After running the long read assembly in Part A, the following steps can be used to evaluate the base level accuracy of the assembled sequence. The Quality Assessment Tool for Genome Assemblies (QUAST) is utilized to compare the assembled consensus sequence to the E.…
Analysis of a whole genome de novo assembly
SeqMan NGen Tutorials » Analysis of a whole genome de novo assembly
DNASTAR Lasergene lets you set up a de novo assembly with ease. One of the outputs is an editable .sqd file that can be opened and edited in SeqMan Ultra. In SeqMan Ultra, you can evaluate the assembled contigs, edit them, organize them into scaffolds, and close any…
Accessing DESeq2 plots from an RNA-Seq assembly
Access and understand output files » Accessing DESeq2 plots from an RNA-Seq assembly
If you perform an RNA-Seq assembly with replicates and specify DESeq2 as the normalization method, SeqMan NGen version 17.6 and later autogenerates editable output files for a variety of plots for genes and isoforms. Looking at plot results can verify whether your data…
The DNASTAR Cloud Data Drive User Interface
Use the DNASTAR Cloud Data Drive » The DNASTAR Cloud Data Drive User Interface
The DNASTAR Cloud Data Drive consists of an upper section with colorful tool icons and a lower section with buttons. The table in the top half of the dialog shows files and folders already being stored in the Cloud. Task How to… To…
Part A: Setting up the assembly in SeqMan NGen
SeqMan NGen Tutorials » Whole genome reference-guided workflow with analysis in ArrayStar » Part A: Setting up the assembly in SeqMan NGen
In this part of the tutorial, you will simply read the steps but won’t follow them yourself. No data are provided, as the data set used is 16 GB in size. Launch SeqMan NGen and choose New Assembly. In the Workflow screen, choose Variant Analysis /…
Permanently Remove Files and Folders from the Cloud
Use the DNASTAR Cloud Data Drive » Permanently Remove Files and Folders from the Cloud
To permanently remove files and/or folders from the DNASTAR Cloud: Select their rows from the upper table by clicking, Shift+clicking or Ctrl/Cmd+clicking. *Note: If nothing is selected, you will receive a warning message after Step 2. Press the Delete…
Add sequences from your computer or the cloud
Add and remove files in the wizard » Add sequences from your computer or the cloud
Some wizard screens require you to add at least one sequence or genome template before proceeding. In these cases, the “Next” button only appears after the item has been added. To add one or more sequences from your computer (i.e. “local”…
Part A: Setting up the transcriptome assembly in SeqMan NGen
SeqMan NGen Tutorials » RNA-Seq de novo transcriptome workflow » Part A: Setting up the transcriptome assembly in SeqMan NGen
In part A of the tutorial, you will use SeqMan NGen to de novo assemble and annotate the RNA-Seq data. Download T5_RNA-Seq_DeNovo_Transcriptome.zip (147 MB) and extract it to any convenient location (i.e., your desktop). The tutorial data consist of the…
Transfer Files from a Physical Computer to the Cloud
Use the DNASTAR Cloud Data Drive » Transfer Files from a Physical Computer to the Cloud
To transfer one or more files from your desktop or laptop computer to the DNASTAR Cloud: Within the Cloud Data Drive, open the folder (if any) that will contain the files you are transferring. *Note: Once a file has been transferred to the DNASTAR Cloud Data…
Transfer a Folder from a Physical Computer to the Cloud
Use the DNASTAR Cloud Data Drive » Transfer a Folder from a Physical Computer to the Cloud
To transfer a folder and its contents from your desktop or laptop computer to the DNASTAR Cloud: Within the Cloud Data Drive, open the folder (if any) that will contain the folder you are transferring. *Note: Once a folder has been transferred to the DNASTAR Cloud…
Create a reference-guided assembly to use in the “SNP to Structure” workflow
Wizard screen descriptions » Workflow » De novo genome assembling and editing workflows » Create a reference-guided assembly to use in the “SNP to Structure” workflow
If you are working with reference-guided human assemblies, Lasergene’s “SNP to Structure” workflow lets you combine genomic sequencing and variant level data with structure files from the RCSB Protein Data Bank (PDB) to model point mutations on the protein…
Part A: Setting up the RNA-Seq reference-guided assembly in SeqMan NGen
SeqMan NGen Tutorials » RNA-Seq reference-guided workflow with analysis in ArrayStar » Part A: Setting up the RNA-Seq reference-guided assembly in SeqMan NGen
In this part of the tutorial, you will learn how to set up the project in SeqMan NGen and (optionally) run the assembly. To perform the assembly in Part A, you must download a 4 GB zipped data folder that unpacks to 14.3 GB. We expect most to simply read this section,…
Transfer Files or Folders from the Cloud to a Physical Computer
Use the DNASTAR Cloud Data Drive » Transfer Files or Folders from the Cloud to a Physical Computer
To download files or folders from the Cloud to a physical computer: Select the files and/or folders from the upper table by clicking, Shift+clicking or Ctrl/Cmd+clicking. *Note: If you do not make a selection, you will receive a warning message after Step…
Preassembly Options for long-read workflows
Wizard screen descriptions » Preassembly Options » Preassembly Options for long-read workflows
*Note: Does your wizard screen look different from the image below? For the standard version of this wizard screen, see Preassembly Options for all other workflows. If your workflow includes the long-read version of the Preassembly Options screen, you can adjust the…
Preassembly Options for all other workflows
Wizard screen descriptions » Preassembly Options » Preassembly Options for all other workflows
*Note: Does your wizard screen look different from the image below? For the standard version of this wizard screen, see Preassembly Options for long-read workflows. If your workflow includes the standard Preassembly Options screen, you can adjust the parameters used…
Input Reference (Sequence, Genome, for Scaffolding, etc.)
Wizard screen descriptions » Input Reference (Sequence, Genome, for Scaffolding, etc.)
If any version of the Reference Sequence screen appears, you must input some type of reference sequence or genome template package before proceeding further in the wizard. The screen has different names depending on the workflow you are following. Some names include:…
Project Report contents for reference-guided workflows
Access and understand output files » View the Project Report » Project Report contents for reference-guided workflows
The Project Report for reference-guided assemblies will contain a subset of the following results: Run Statistics Reference Seq Cnt The total number of sequences in the reference (template). Sequence Cnt The total number of reads…
Project Report contents for de novo workflows
Access and understand output files » View the Project Report » Project Report contents for de novo workflows
The Project Report for de novo assemblies will contain a subset of the following results: Assembly Totals Contigs Total number of contigs assembled. Contigs > 2K Total number of assembled contigs that are more than 2000 base pairs…
Specify a VCF, BED or Manifest file
Wizard screen descriptions » Input Reference (Sequence, Genome, for Scaffolding, etc.) » Specify a VCF, BED or Manifest file
Certain workflows allow or require you to import a BED file, Manifest file, or a custom VCF SNP file with data from one or more assemblies. These options, if available, will be offered at the bottom of the Reference Sequence screen. To add a BED, Manifest, or…
Templated long-read workflow (ARTIC)
SeqMan NGen Tutorials » Templated long-read workflow (ARTIC)
As described in the ARTIC Amplicon workflow topic, many researchers working with viral genomes will start with draft genomes, while some will start with raw (unassembled) Nanopore or PacBio long-read data that requires assembly. This tutorial is in two parts, one for…
Wizard screen descriptions
Wizard screen descriptions
SeqMan NGen’s project setup wizard lets you upload files and optimize parameters for your assembly. After choosing your desired workflow in the first (“Workflow”) screen, subsequent wizard screens will vary according to the workflow chosen. Most…
ChIP-Seq workflow with analysis in ArrayStar
SeqMan NGen Tutorials » ChIP-Seq workflow with analysis in ArrayStar
Lasergene Genomics’ ChIP-Seq analysis workflow enables you to locate the binding sites of DNA-associated proteins and determine how these proteins interact with the DNA to affect expression in nearby genes. In this tutorial, you will use SeqMan NGen to create a…
Whole genome reference-guided workflow with analysis in ArrayStar
SeqMan NGen Tutorials » Whole genome reference-guided workflow with analysis in ArrayStar
In this tutorial, you will look for deleterious genes in the Caucasian/Utah/Mormon father-mother-daughter trio data from the NIST Genome in a Bottle project. This is commonly referred to as the “CEPH Trio.” No data are provided for Part A of the tutorial.…
Include DESeq2 or edgeR statistics
Wizard screen descriptions » Workflow » RNA-seq/transcriptomics workflows » Include DESeq2 or edgeR statistics
To view statistics from DESeq2 or edgeR in ArrayStar, you first need to create one or more SeqMan NGen assembles in which one of these statistical packages was specified as the normalization method. That specification also triggers the use of the package for…
saveProject
Appendix » Run SeqMan NGen through the command line » SNG commands » Project management commands » saveProject
The saveProject command saves the assembly to a project file. By default, the SeqMan Pro / SeqMan Ultra project file format (.sqd) is used. Phrap (.ace) and FASTA (.fas) formats may also be specified by using the format parameter, and specifying the desired file…
Welcome
Wizard screen descriptions » Welcome
Each time you launch SeqMan NGen, the first screen that appears is the “Welcome” screen. The top of the screen has two option buttons. Press New Assembly to set up and run an assembly project using the SeqMan NGen wizard. You will start at the…
Input Assemblies
Wizard screen descriptions » Input Assemblies
If you are following a Combine/Reanalyze Existing Assemblies workflow, you must input at least two assemblies into the Input Assemblies screen before proceeding to the next wizard screen. *Note: This screen is different from the similarly-named Input Assembly screen,…
setParam
Appendix » Run SeqMan NGen through the command line » SNG commands » Parameter settings commands » setParam
The setParam command allows you to adjust the stringency of one or more of the assembling parameters for the project. SeqMan NGen will use the default values for any parameter that is not specified within the script. Parameter Description Allowed values…
Whole genome de novo workflow with mate pair data
SeqMan NGen Tutorials » Whole genome de novo workflow with mate pair data
In this tutorial, you will use SeqMan NGen to de novo assemble an E. coli K12 MG155 data set composed of Illumina MiSeq (2×300) paired end reads. The default stringency setting is designed to produce longer contigs; however, some may contain false joins.…
How “mer tags” are chosen
Appendix » SeqMan NGen calculations » How “mer tags” are chosen
The SeqMan NGen layout algorithm relies on unique subsequences of bases, or mers, which occur in overlapping regions of fragment reads. Mers that are common to two or more fragment reads are aligned to determine the overall layout of reads. Overlapping reads have many…
De novo workflow output
Access and understand output files » De novo workflow output
De novo workflows output a results folder containing the following files: File Suffix Description .sqd The main assembly output. To view and analyze the assembly, open this file with SeqMan Pro or SeqMan Ultra. .txt …
Contents of the -reports folder
Access and understand output files » Reference-guided workflow output » Contents of the .assembly package » Contents of the -reports folder
The -reports folder is part of the XNG .assembly package. In the table below (and in the sentence above), it should be understood that the project name precedes any hyphen (-) or period (.) used at the beginning of file and folder names. File Suffix or…
Part A: Setting up the CNV project in SeqMan NGen
SeqMan NGen Tutorials » Copy number variation (CNV) workflow with analysis in ArrayStar and GenVision Pro » Part A: Setting up the CNV project in SeqMan NGen
In this part of the tutorial, you will use the SeqMan NGen wizard to import data and run the assembly. You will then press a button to open the results in ArrayStar. Download T3_CNV.zip (1.4 GB) and extract the contents to any convenient location (e.g., your…
De novo genome assembling and editing workflows
Wizard screen descriptions » Workflow » De novo genome assembling and editing workflows
The following table describes each of the workflows available in the De novo genome assembly and editing tab of the Workflow screen. Group Workflow Description ABI / Sanger De novo assembly Fast, accurate trimming and assembly of…
(Short Read) Polishing Options
Wizard screen descriptions » (Short Read) Polishing Options
This screen appears in long read workflows and pertains to the short read sequences being used to refine a long-read assembly. Some workflows call this the Polishing Options screen, while others call it the Short Read Polishing Options screen, but both screens are…
Part A: Creating draft genomes in SeqMan NGen and exporting a consensus from SeqMan Ultra
SeqMan NGen Tutorials » Templated long-read workflow (ARTIC) » Part A: Creating draft genomes in SeqMan NGen and exporting a consensus from SeqMan Ultra
In Part A of this tutorial, you will use raw data in PacBio CLR, PacBio HiFi or Nanopore format to create draft genome assemblies for seven SARS-CoV-2 samples using SeqMan NGen. You will then open one of the assemblies in SeqMan Ultra, generate a table of…
Reference-guided workflow output
Access and understand output files » Reference-guided workflow output
Reference-guided workflows vary in the number and contents of output files and folders. Only a subset of items in the table below may appear for a particular workflow. In the file names below, the project name should be understood to precede any hyphen (-) or…
Contents of the -zinternal folder
Access and understand output files » Reference-guided workflow output » Contents of the .assembly package » Contents of the -reports folder » Contents of the -zinternal folder
The -zinternal folder is located in the -reports folder, which in turn is part of the XNG .assembly package. In the table below (and the nomenclature used in the sentence above), it should be understood that the project name precedes any hyphen (-) or period (.)…
Combine/Reanalyze Existing Assemblies
Wizard screen descriptions » Workflow » Combine/Reanalyze Existing Assemblies
The following table describes each of the workflows available in the Combine/Reanalyze Existing Assemblies tab of the Workflow screen. Group Workflow Description Combine/Reanalyze Combine existing assemblies Once you have prepared…
removeSmallContigs
Appendix » Run SeqMan NGen through the command line » SNG commands » Preprocessing and assembling commands » removeSmallContigs
The removeSmallContigs command disassembles any contigs without reference sequences that have fewer than the specified number of sequences. Parameter Description Allowed values minLength Specifies the minimum length of a contig to prevent…
Make a custom VCF file
Wizard screen descriptions » Input Reference (Sequence, Genome, for Scaffolding, etc.) » Specify a VCF, BED or Manifest file » Make a custom VCF file
Variant Call Format (VCF) files have multiple uses. For instance, they can provide a way to flag previously known SNPs and to filter them in SNP tables. In DNASTAR’s SeqMan NGen, these SNPs are called "annotated SNPs"; in ArrayStar, they are referred to as "user…
ARTIC Amplicon workflow
Wizard screen descriptions » Workflow » Variant Analysis/Resequencing workflows » ARTIC Amplicon workflow
Starting with the release of Lasergene 17.3 (2021), SeqMan NGen supports both templated and de novo assembly of long-read data from Oxford Nanopore Technologies (ONT), Pacific Biosciences (PacBio) CLR and PacBio HiFi. The templated long-read workflow, known as…
Handling of sex chromosomes
Appendix » SeqMan NGen calculations » Handling of sex chromosomes
When using the SeqMan NGen wizard, certain workflows allow you to specify the subject’s Gender in the Assembly Options screen. *Note for command-line users: When using the command-line version of XNG, the sex of the subject is instead specified using the…
assembleTemplate
Appendix » Run SeqMan NGen through the command line » XNG commands » assembleTemplate
*Note: All parameters are assumed to be optional unless the description is prefaced by “required.” assembleTemplate is a required command, and Initiates the assembly of the loaded sequences using the specified template as a reference. Example: XNG script used…
Whole genome reference-guided workflow
SeqMan NGen Tutorials » Whole genome reference-guided workflow
In this tutorial, you will create a reference-guided assembly using SeqMan NGen and then analyze the results using SeqMan Ultra. The time required for the assembly component is approximately 2-5 minutes. Running a reference-guided assembly in SeqMan NGen: Download…
Welcome to SeqMan NGen
Welcome to SeqMan NGen
Lasergene Genomics provides everything you need for assembly and analysis of genomic, metagenomic, exomes/gene panels and transcriptomic sequencing data, and supports all popular file formats. Most workflows will start with sequence assembly in SeqMan NGen. SeqMan…
Add and remove files in the wizard
Add and remove files in the wizard
Many wizard screens allow or require you to specify files that will be used in the assembly. There are several ways to add these files, each discussed in a separate topic: Add sequences from your computer or the cloud Add a genome template from DNASTAR Add a…
Remove PhiX control reads from Illumina data prior to import
Wizard screen descriptions » Workflow » De novo genome assembling and editing workflows » Remove PhiX control reads from Illumina data prior to import
During de novo assembly, contamination of Illumina data with PhiX control sequence may result in the generation of spurious contigs. For background information, see Mukherjee et al., 2015. Note that: Not all Illumina data are contaminated with PhiX. PhiX…
RNA-seq/transcriptomics workflows
Wizard screen descriptions » Workflow » RNA-seq/transcriptomics workflows
The following table describes each of the workflows available in the RNA-seq/transcriptomics tab of the Workflow screen. Group Workflow Description Quantitative analysis RNA-seq RPKM gene expression quantification and differential…
dumpSNP
Appendix » Run SeqMan NGen through the command line » XNG commands » dumpSNP
The command dumpSNP is intended for internal use only, and creates a tab delimited text file from one or more SNP containing binary files generated during assembly. SNP binary files include those with the .snpExt suffix contained in an .assembly package as well as…
Set Contaminant
Wizard screen descriptions » Set Contaminant
If you are following certain RNA-Seq workflows, the wizard includes the Set Contaminant screen. The screen prompts you to remove rRNA sequences if they are present. We highly encourage doing so, as these sequences can represent up to 80% of the reads in a de novo…
Specify read technology
Wizard screen descriptions » Input Sequences » Specify read technology
To specify read technology in the Input Sequences screen, make a selection from the Read technology drop-down menu. Default values for parameters and other assembly options in subsequent panels will be based on this selection. Considerations when choosing a read…
RNA-Seq reference-guided workflow output
Access and understand output files » RNA-Seq reference-guided workflow output
If you are following a reference-guided RNA-Seq workflow, output results are saved in an .assembly package folder labeled with the user-specified project name and the suffix _RNA-Seq. This folder contains the following files: Subfolder Name File…
Variants tab
Wizard screen descriptions » Options tabs » Variants tab
The Variants tab is used to set parameters for the variant analysis phase of the assembly. To access the tab from the Analysis Options screen, click the Advanced Analysis Options button then click on the Variants tab. The options available in this tab vary depending on…
Variant Analysis/Resequencing workflows
Wizard screen descriptions » Workflow » Variant Analysis/Resequencing workflows
The following table describes each of the workflows available in the Variant Analysis/Resequencing tab of the Workflow screen. Group Workflow Description ABI / Sanger Whole genome Align Sanger trace data from one or multiple samples…
RNA-seq normalization methods
Wizard screen descriptions » Analysis Options » RNA-seq normalization methods
“Normalization” refers to the standardization of sequencing data on the basis of sequencing depth and gene length. Some versions of the Assembly Options screen allow you to specify a data normalization method, or to select None, in which case data will not be…
RNA-Seq reference-guided workflow with analysis in ArrayStar
SeqMan NGen Tutorials » RNA-Seq reference-guided workflow with analysis in ArrayStar
RNA-Seq uses next-gen sequencing to show the presence and quantity of RNA in a genome at a particular moment. DNASTAR’s SeqMan NGen application is the starting point for both reference-guided and de novo RNA-Seq workflows. Because this tutorial involves a…
Analysis Options
Wizard screen descriptions » Analysis Options
The Analysis Options wizard screen allows you to specify the analysis parameters to use for your assembly. This screen comes in several variations, one of which is shown below: !Important: If you are setting up a gene homology alignment in MegAlign Pro or following…
Long-read analysis with accuracy evaluation
SeqMan NGen Tutorials » Long-read analysis with accuracy evaluation
The following tutorial shows how to do long read assembly in SeqMan NGen, and contains optional steps for assembly validation in QUAST (Quality Assessment Tool for Genome Assemblies). The sequence data consists of an Oxford Nanopore Technologies (ONT) MAP006-1 .fastq…
Include gene set enrichment analysis (GSEA) statistics
Wizard screen descriptions » Workflow » RNA-seq/transcriptomics workflows » Include gene set enrichment analysis (GSEA) statistics
With the release of Lasergene 18, SeqMan NGen’s templated RNA-Seq workflow supports gene set enrichment analysis (GSEA), a computational method provided by a collaboration of University of California-San Diego and The Broad Institute (Subramanian et al.,…
dumpConsensus
Appendix » Run SeqMan NGen through the command line » XNG commands » dumpConsensus
The command dumpConsensus is intended for internal use only, and is used to convert the binary consensus file created during assembly into a text file. Parameter Description Allowed values (defaults underlined) file Specifies the…
Workflow
Wizard screen descriptions » Workflow
“Workflow” is the first wizard screen in SeqMan NGen and is where you select the assembly workflow. Each group of workflows is accessed by clicking its dark blue “bar-shaped” tab on the left. Click a link below for descriptions of each…
Input Contig Sequences
Wizard screen descriptions » Input Contig Sequences
If you select a Genome finishing or Genome polishing workflow from the Workflow screen, the Input Contig Sequences screen will be included in the wizard. You must enter one or more data files in this dialog before proceeding to the next screen. To use the consensus…
Part B: Analyzing the results in ArrayStar
SeqMan NGen Tutorials » Whole genome reference-guided workflow with analysis in ArrayStar » Part B: Analyzing the results in ArrayStar
In Part A of this tutorial, you read about how the SeqMan NGen assembly project was set up. In this part, you will download the CEPH Trio.astar assembly results file and perform downstream analysis in ArrayStar. ArrayStar is a discovery tool that provides many…
exportSplits
Appendix » Run SeqMan NGen through the command line » XNG commands » exportSplits
The command exportSplits is intended for internal use only, and is used to convert the binary splits file created during assembly into a text file. Parameter Description Allowed values file Specifies the directory and file/folder. …
Specify single sample, multi-sample or replicate data
Wizard screen descriptions » Input Sequences » Specify single sample, multi-sample or replicate data
Depending on the workflow, the Input Sequences screen may include an Experiment setup drop-down menu. You must make a selection from this menu before proceeding to the next screen. To run each sample individually: Specify the Read technology using the drop-down…
assemble
Appendix » Run SeqMan NGen through the command line » SNG commands » Preprocessing and assembling commands » assemble
The assemble command is required and reprocesses and assembles the sequences that have been loaded. Preprocessing may include quality trimming, and scanning for vector, repetitive, and contaminant sequences. Parameter Description Allowed values…
Handling of repeats
Appendix » SeqMan NGen calculations » Handling of repeats
Repeat handling parameters compute a threshold for deciding the number of identical subsequences of bases (mers) used to indicate a putative repeat. Mers that are common to two or more fragment reads are aligned to determine the overall layout of reads. For additional…
Add a genome template from NCBI
Add and remove files in the wizard » Add a genome template from NCBI
If your workflow includes the Reference Sequence or Set Contaminant screen, you must add at least one reference sequence, biome genome, or genome template before proceeding. If you are doing a local (i.e. non-Cloud) assembly, you may download and/or add genomes…
View the Project Report
Access and understand output files » View the Project Report
The Project Report summarizes the assembly statistics, including the parameters used, the number of assembled/unassembled sequences and contigs in your project, and the average quality scores. Opening the Project Report: Use any of the methods below: Click the…
XNG, SNG, and QNG assemblers
Appendix » Run SeqMan NGen through the command line » XNG, SNG, and QNG assemblers
SeqMan NGen uses three powerful assemblers: XNG, SNG and QNG. The XNG assembler: The XNG assembler (patent pending) is used for all reference-guided assemblies. This assembler features an algorithm for fast, accurate assembly of extremely large genomes and is…
Part B: Analyzing the results in ArrayStar using quick gene sets
SeqMan NGen Tutorials » RNA-Seq reference-guided workflow with analysis in ArrayStar » Part B: Analyzing the results in ArrayStar using quick gene sets
In Part A of this tutorial, you set up and ran a templated RNA-Seq assembly using SeqMan NGen. In this part of the tutorial, you will analyze assembly results in ArrayStar using a “quick gene set” and the Gene Table to locate a potential operon…
Detection of structural variations
Appendix » SeqMan NGen calculations » Detection of structural variations
In addition to SNPs and small insertions and deletions, genetic variation can also involve large scale rearrangements. These rearrangements may include large insertions and deletions, inversions, and translocations — collectively known as structural variations…
Peak Detection tab
Wizard screen descriptions » Options tabs » Peak Detection tab
The Peak Detection tab is used to set parameters for MACS peak detection. To access the tab from the Analysis Options screen, click the Advanced Analysis Options button then click on the Peak Detection tab. The options available in this tab may vary depending on the…
Scans tab
Wizard screen descriptions » Options tabs » Scans tab
The Scans tab is used to set scanning parameters. The tab can be accessed in either of two ways: From the Assembly Options screen, click the Advanced Options button then click on the Scans tab. From the Preassembly Options screen, click the Advanced Options…
Trimming tab
Wizard screen descriptions » Options tabs » Trimming tab
This is the disambiguation page for “Trimming tab.” In SeqMan NGen, there are two advanced options dialogs that contain a Trimming tab. See the topics below for information about each version of this tab. If you reached the Trimming tab this…