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).