Set pair information, if paired

500

3000

user defined

no pairs allowed

5000

Assembly Options

Mer size – miRNA only

15

Mer size – Templated Metagenomic only

21

21

19

21

25

21

Mer size – All others

21

21

19

21

25

21

Minimum match percentage – Templated Metagenomic only

99

Minimum match percentage – all others

93

85

93

80

90

90

Variant detection mode

user defined

SNP filter stringency

low

Advanced Options

Alignment Tab

Minimum aligned length – miRNA only

17

Minimum aligned length – metagenomics only

50

100

100

100

50

50

Minimum aligned length – all others

35

50

25

100

50

50

Maximum gap size

6 (miRNA only)

30 (all others)

Maximum total reads

false (when true, default is 10,000,000)

Auto trim reads

true

Trim to targeted regions

false

Combine duplicate reads

true

Remove clonal reads

paired reads = false

unpaired reads = disabled

Place repeat reads

Place all (Metagenomics)

Place once (all others)

Variant Tab

Filter stringency

This selection controls the three “editable variant filters” shown in the columns below:

Minimum variant percentage (fixed)

1 (Metagenomics-templated w/host removal only)

5 (all others)

P not ref (fixed)

Disabled (Metagenomics and Exome)

10 (all others)

Minimum variant count

2

Minimum base quality score

20 (Metagenomics only)

5 (all others)

Minimum strand coverage

5 (Metagenomics and Exome only)

0 (all others)

Somatic/cancer/heterogeneous SNP caller

0.25

Maximum strand bias – haploid/diploid only

user defined

0.8

0.8

user defined

user defined

user defined

Bases to mask at ends of reads

5 (Somatic/cancer/heterogeneous SNP caller only)

0 (all others)

Bayesian-based removal of heterozygous indels

false

true

true

false

false

false

Additional Tab (internal use only)

Maximum repeat count

100

Assembly output format

SeqMan document disabled (Reference-guided with gap closure only)

BAM assembly package (all others)

Limit deep regions

True (miRNA only)

false

Minimum match percentage – Metagenomics only

99

Minimum match percentage – all others

90

Match score

10

Mismatch penalty

20

Gap penalty

50

Gap extension penalty – miRNA only

30

Gap extension penalty – Exome only

5

10

10

5

5

5

Gap extension penalty – all others

5

10

10

5

5

5

Alignment cutoff

100 (miRNA only)

200 (all others)

Favor 5’ gap

true

Check strands

false

Maximum length – haploid/diploid

user defined

Maximum length – heterogeneous

5

3

3

5

5

5

Minimum homopolymer fraction

0

Depth

0