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1 .TH wgsim 1 "21 June 2017" "samtools-1.5" "Bioinformatics tools"
2 .SH NAME
3 wgsim \- Whole-genome sequencing read simulator
4 .SH SYNOPSIS
5 .B wgsim
6 [\fI\,options\/\fR] \fI\,<in.ref.fa> <out.read1.fq> <out.read2.fq>\/\fR
7 .PP
8 <in.ref.fa> must be a fasta file containing a reference genome.
9 .PP
10 <out.read1.fq> and <out.read2.fq> are the first and second read output files.
11 .SH OPTIONS
12 .TP
13 \fB\-e\fR FLOAT
14 base error rate [0.000]
15 .TP
16 \fB\-d\fR INT
17 outer distance between the two ends [500]
18 .TP
19 \fB\-s\fR INT
20 standard deviation [50]
21 .TP
22 \fB\-N\fR INT
23 number of read pairs [1000000]
24 .TP
25 \fB\-1\fR INT
26 length of the first read [70]
27 .TP
28 \fB\-2\fR INT
29 length of the second read [70]
30 .TP
31 \fB\-r\fR FLOAT
32 rate of mutations [0.0010]
33 .TP
34 \fB\-R\fR FLOAT
35 fraction of indels [0.15]
36 .TP
37 \fB\-X\fR FLOAT
38 probability an indel is extended [0.30]
39 .TP
40 \fB\-S\fR INT
41 seed for random generator [\-1]
42 .TP
43 \fB\-A\fR FLOAT
44 discard if the fraction of ambiguous bases higher than FLOAT [0.05]
45 .TP
46 \fB\-h\fR
47 haplotype mode
48 .TP
49 Parameter defaults are given in square brackets.
50 .SH AUTHOR
51 Copyright 2008 Genome Research Limited.
52 .br
53 Copyright 2011 Heng Li.
54 .TP
55 wgsim is part of samtools, https://github.com/samtools/samtools