---
name: "mapsembler2_kissreads"
section: "1"
platform: "linux"
package: "mapsembler2"
version: "2.2.4+dfsg1-4"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/mapsembler2_kissreads"
---

# mapsembler2\_kissreads(1)

Checks for each sequence contained into the toCheck.fasta if it is read coherent with reads from readsA.fasta or readsB.fasta

## 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

## SYNOPSIS

**mapsembler2\_kissreads** \<toCheck.fasta\> \<readsC1.fasta\> \[\<readsC2.fasta\> \[\<readsC3.fasta\] ...\] \[-k value\] \[-c value\] \[-d value\] \[-O value\] \[-o name\] \[-u name\] \[-n\] \[-I\] \[-i index\_stride\] \[-m align\_file\] \[-s\] \[-f\] \[-h\]

## 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:

-

  if (s coherent with at least one read set): output the sequence as follows

-

  \>original fasta comment\|C1:min\<avg-corr\_avg\<max\|C2:min\<avg-cor\_avg\<max\|C3...: \>s

-

  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

## OPTIONS

**-k** size\_seed: will use seeds of length size\_seed. Default: 25.

**-O** minimal\_read\_overlap: a read can be mapped if its overlap is a least "minimal\_read\_overlap". Default: k

**-c** min\_coverage: a sequence is covered by at least min\_coverage coherent reads. Default: 2

**-d** 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.

**-o** file\_name: write read-coherent outputs. Default: standard output

**-u** file\_name: write unread-coherent outputs. Default: standard output

**-n** the input file (toCheck.fasta) is a kissnp output (incompatible with **-I** option)

-

  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 substitution is authorized on this position.

**-I** the input file (toCheck.fasta) is an Intl output (incompatible with **-n** option)

**-i** 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)

**-t** max number of threads (also limited by number of input files)

**-m** align\_file, write a file of reads mapped to sequences in file align\_file

**-s** silent mode

**-f** outputs coherent events in a standard fasta file format

**-h** prints this message and exit

## AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.