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 <[email protected]>, for the Debian project (but may be used by others).