.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.7.
.TH MAPSEMBLER2_KISSREADS "1" "October 2018" "mapsembler2_kissreads 2.2.4" "User Commands"
.SH NAME
mapsembler2_kissreads \- Checks for each sequence contained into the toCheck.fasta if it is read coherent with reads from readsA.fasta or readsB.fasta
.SH SYNOPSIS
.B mapsembler2_kissreads
<toCheck.fasta> <readsC1.fasta> [<readsC2.fasta> [<readsC3.fasta] ...] [\-k value] [\-c value] [\-d value] [\-O value] [\-o name] [\-u name] [\-n] [\-I] [\-i index_stride] [\-m align_file] [\-s] [\-f] [\-h]
.SH DESCRIPTION
Checks for each sequence contained into the toCheck.fasta if
it is read coherent (each position is covered by at least "min_coverage" read(s)) with reads from readsA.fasta or readsB.fasta
A sequence s from toCheck is treated as follow:
.IP
if (s coherent with at least one read set): output the sequence as follows
.IP
>original fasta comment|C1:min<avg\-corr_avg<max|C2:min<avg\-cor_avg<max|C3...:
>s
.IP
With A:min<avg\-cor_avg<max standing for : value of the position having minimal coverage in readsA.fasta < average coverage in readsA.fasta \- R\-squarred corrected average in readsA.fa < value of the position having maximal coverage in readsA.fasta
The coverage is the number of reads that perfectly mapped a position
Any other situation (s not coherent with any): couple non read coherent, not outputed
.SH OPTIONS
.HP
\fB\-k\fR size_seed: will use seeds of length size_seed. Default: 25.
.HP
\fB\-O\fR minimal_read_overlap: a read can be mapped if its overlap is a least "minimal_read_overlap". Default: k
.HP
\fB\-c\fR min_coverage: a sequence is covered by at least min_coverage coherent reads. Default: 2
.HP
\fB\-d\fR max_substitutions: Maximal number of substitutions authorized between a read and a fragment. Note that no substitution is allowed on the central position while anaylizing the kissnp output. Default: 1.
.HP
\fB\-o\fR file_name: write read\-coherent outputs. Default: standard output
.HP
\fB\-u\fR file_name: write unread\-coherent outputs. Default: standard output
.HP
\fB\-n\fR the input file (toCheck.fasta) is a kissnp output (incompatible with \fB\-I\fR option)
.IP
in this case: 1/ only the upper characters are considered (no mapping done on the extensions) and 2/ the central position (where the SNP occurs) is strictly mapped, no subsitution is authorized on this position.
.HP
\fB\-I\fR the input file (toCheck.fasta) is an Intl output (incompatible with \fB\-n\fR option)
.HP
\fB\-i\fR index_stride (int value). This is a heuristic for limiting the memory footprint. Instead of indexing each kmer of the sequences contained into the toCheck.fasta, kissreads indexes kmers occurring each "index_stride" position. Default = 1 (no heuristic)
.HP
\fB\-t\fR max number of threads (also limited by number of input files)
.HP
\fB\-m\fR align_file, write a file of reads mapped to sequences in file align_file
.HP
\fB\-s\fR silent mode
.HP
\fB\-f\fR outputs coherent events in a standard fasta file format
.HP
\fB\-h\fR prints this message and exit
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.