seqcons1
Multi-read alignment
Usage
seqcons -r
<FASTA
file
with
reads>
[Options]
Overview
Multi-read alignment - SeqCons
-
seqcons
-a<AMOS message file> [Options]
-
-h, --help -
displays this help message
-
-V, --version -
print version information
Main Options:
-r,--reads<FASTA reads file>-
file with reads
-a,--afg<AMOS afg file>-
message file
-
-o, --outfile <Filename> -
output filename (default align.txt)
-f,--format[seqan | afg]-
output format (default afg)
-m,--method[realign | msa]-
alignment method (default realign)
-
-b, --bandwidth <Int> -
bandwidth (default 8)
-
-n, --noalign -
no align, only convert input
MSA Method Options:
-
-ma, --matchlength <Int> -
min. overlap length (default 15)
-
-qu, --quality <Int> -
min. overlap precent identity (default 80)
-
-ov, --overlaps <Int> -
min. number of overlaps per read (default 3)
-
-wi, --window <Int> -
window size (default 0) /*If this parameter is > 0 then all
-
overlaps within a given window are computed.*/
ReAlign Method Options:
-
-in, --include -
include contig sequence
-rm,--rmethod[nw | gotoh]-
realign method (default gotoh)