Save Project As

SeqMan Format 10M read limit Editable

Save Unassembled Reads

False

Save Contigs To FASTA

False (Special Reference-Guided only)

True (all others)

Save Report

True

Set Pair Information, if paired

500

3000

User defined

No pairs allowed

3000

5000

Discard reads without linkers

N/A

True

True

N/A

N/A

N/A

Read Options

Maximum total reads

10000000

Quality end trim

True

True

True

False

True

True

Vector/adaptor scan

False

Contaminant scan

False

Repeat scan

False

Advanced Trim/Scan Options

Quality End Trimming

Minimum quality

20

20

20

5

20

20

Window

5

5

10

5

5

5

Fixed End Trimming

Do fixed end trimming

False

5’ Trim

Disabled

3’ Trim

Disabled

3’ Value is measured from 5’ end

Disabled

Other End Trimming Options

Trim to mer

False

False

True

True

False

False

Remove Small Reads

Remove small reads

False

Minimum length

Disabled

Vector/Adaptor Scan

Mer length

9

Minimum matches

3

Trim length

30

Trim to end

25

Repeat Scan

Mer length

17

Minimum matches

2

Flag length

50

Contaminant Scan

Mer length

17

Minimum matches

12

Assembly Options

Repeat handling

True (De Novo Genome)

False (De Novo Metagenomics and miRNA)

Disabled (All others)

Expected genome length

Disabled (Transcriptome)

0 (All others)

Expected coverage

Disabled (Transcriptome)

20 (All others)

Mer size – Genome and Transcriptome only

21

21

19

21

25

21

Mer size – miRNA

15

Minimum match percentage – Metagenomic only

99

99

99

99

99

99

Minimum match percentage – all others

93

85

93

80

90

90

Realign reads after assembly

True (De Novo Genome, Special Reference-Guided)

False (All others)

De novo assemble remaining unassembled reads

False (Special Reference-Guided only)

Disabled (All others)

Split template at zero coverage

False (Reference-guided with gap closure)

Disabled (All others)

Remove small contigs after assembly

False (transcript annotation workflow)

True (all others)

Minimum sequences

100

10

10

10

10

10

Minimum length

0

Advanced Assembly Options

Match score

10

Mismatch penalty

20

Gap penalty

30

Max gap – miRNA only

6

Max gap – All others

6

15

15

30

15

15

SNP passes

2

SNP match percent

90

SNP low cover cutoff

0

Match window

50

50

50

100

50

50

Maximum coverage

0

Match repeat percent

150

Match spacing

50

75

20

150

150

10

Default quality

15

Default template quality

500

Max usable

25

Genome ploidy (only if ‘Save project as BAM format’ is checked

Population/other (De novo Metagenomics only)

Diploid (all others)