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kissreads - Online in the Cloud

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This is the command kissreads that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

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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