seqcons(1) Multi-read alignment


seqcons -r <FASTA file with reads> [Options]


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)


seqcons was written by Tobias Rausch

This manual page was generated using html2man and polished by Soeren Sonnenburg <[email protected]>, for the Debian project (but may be used by others).