Parameters Illumina 454 Ion Torrent Pac Bio Sanger Other
Set pair information, if paired 500 3000 user defined no pairs allowed 5000 5000
Assembly Options
Mer size – miRNA only 15
Mer size – Reference-guided Metagenomic only 21 21 19 21 25 21
Mer size – All others 21 21 19 21 25 21
Minimum match percentage – Reference-guided 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
Maximum strand bias – haploid/diploid only user defined 0.8 0.8 user defined user defined user defined
Bayesian-based removal of heterozygous indels false true true false false false
Filter stringency This selection controls the three “editable variant filters” shown in the table immediately following this table.
Minimum variant percentage (fixed) 1 (Metagenomics-reference-guided 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
Bases to mask at ends of reads 5 (Somatic/cancer/heterogeneous SNP caller only)
0 (all others)
Additional Tab* (internal use only)
Assembly output format SeqMan document disabled (Reference-guided with gap closure only)
BAM assembly package (all others)
Limit deep regions true (miRNA only)
false (all others)
Maximum repeat count 100
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

The table below shows the editable variant filters (“Filter Stringency”):

Stringency Minimum variant percentage PnotRef Depth
low 15 90 20
medium 15 99 20
high 15 99.9 20
custom 5 (Exome & Metagenomics reference-guided w/host removal)
25 (all others)
Disabled (Exome & Metagenomics reference-guided w/host removal)
90 (all others)
25 (Exome & Metagenomics reference-guided w/host removal)
20 (all others)

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