seqcons(1)

seqcons1

Multi-read alignment

Usage

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

Overview

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)

Releases

Unchanged in 2 releases since Debian 6.0 (Squeeze).

6.0–7

$ seqcons

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