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
all
- overlaps 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).