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
Parameters Illumina 454 Ion Torrent Pac Bio Sanger Other
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
Quality end trim True True True False True True
Maximum total reads 10000000
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
Mer size – Genome and Transcriptome only 21 21 19 21 25 21
Minimum match percentage – Metagenomic only 99 99 99 99 99 99
Minimum match percentage – all others 93 85 93 80 90 90
Minimum sequences 100 10 10 10 10 10
Mer size – miRNA 15
Expected genome length Disabled (Transcriptome)
0 (All others)
Expected coverage Disabled (Transcriptome)
20 (All others)
Repeat handling True (De Novo Genome)
False (De novo Metagenomics and miRNA)
Disabled (All others)
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 length 0
Advanced Assembly Options
Match window 50 50 50 100 50 50
Match spacing 50 75 20 150 150 10
Genome ploidy (only if Save project as BAM format is checked) Population/other (De novo Metagenomics only)
Diploid (all others)
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
Maximum coverage 0
Match repeat percent 150
Default quality 15
Default template quality 500
Max usable 25

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