.TH SEQCONS "1" "September 2009" "Version 0.22 (06. August 2009) Revision: 4663" "User Commands"
.SH NAME
seqcons \- Multi\-read alignment
.SH SYNOPSIS
.B seqcons
\fI-r <FASTA file with reads> \fR[\fIOptions\fR]
.SH DESCRIPTION
Multi\-read alignment \- SeqCons
.IP
seqcons \fB\-a\fR <AMOS message file> [Options]
.TP
\fB\-h\fR,  \fB\-\-help\fR
displays this help message
.TP
\fB\-V\fR,  \fB\-\-version\fR
print version information
.SS "Main Options:"
.TP
\fB\-r\fR,  \fB\-\-reads\fR <FASTA reads file>
file with reads
.TP
\fB\-a\fR,  \fB\-\-afg\fR <AMOS afg file>
message file
.TP
\fB\-o\fR,  \fB\-\-outfile\fR <Filename>
output filename (default align.txt)
.TP
\fB\-f\fR,  \fB\-\-format\fR [seqan | afg]
output format (default afg)
.TP
\fB\-m\fR,  \fB\-\-method\fR [realign | msa]
alignment method (default realign)
.TP
\fB\-b\fR,  \fB\-\-bandwidth\fR <Int>
bandwidth (default 8)
.TP
\fB\-n\fR,  \fB\-\-noalign\fR
no align, only convert input
.SS "MSA Method Options:"
.TP
\fB\-ma\fR, \fB\-\-matchlength\fR <Int>
min. overlap length (default 15)
.TP
\fB\-qu\fR, \fB\-\-quality\fR <Int>
min. overlap precent identity (default 80)
.TP
\fB\-ov\fR, \fB\-\-overlaps\fR <Int>
min. number of overlaps per read (default 3)
.TP
\fB\-wi\fR, \fB\-\-window\fR <Int>
window size (default 0)
/*If this parameter is > 0 then all
.IP
overlaps within a given window
are computed.*/
.SS "ReAlign Method Options:"
.TP
\fB\-in\fR, \fB\-\-include\fR
include contig sequence
.TP
\fB\-rm\fR, \fB\-\-rmethod\fR [nw | gotoh]
realign method (default gotoh)
.SH AUTHOR
.br
seqcons was written by Tobias Rausch
.PP
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