kissreads - Online in the Cloud

PROGRAM:

NAME

kissreads - manual page for kissreads 1.2.6

DESCRIPTION

NAME kissReads, version kissreads module 1.2.6 - Copyright INRIA - CeCILL License

SYNOPSIS kissreads/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 subsitution 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

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