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MAPSEMBLER2_KISSREADS(1) User Commands MAPSEMBLER2_KISSREADS(1)

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.
October 2018 mapsembler2_kissreads 2.2.4