SEQCONS(1)
NAME
seqcons - Multi-read alignment
SYNOPSIS
seqcons -r <FASTA file with reads> [Options]
DESCRIPTION
- 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 alloverlaps within a given window are computed.*/
- ReAlign Method Options:
- -in, --include
include contig sequence
- -rm, --rmethod [nw | gotoh]
realign method (default gotoh)
AUTHOR
seqcons was written by Tobias Rausch
- This manual page was generated using html2man and polished by Soeren
Sonnenburg <sonne@debian.org>, for the Debian project (but may be used
by others).