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kissreads - manual page for kissreads 1.0.1
This is kissreads, version 1.3.2 - Copyright INRIA - CeCILL License The command line was: kissreads/kissreads -h NAME kissReads, version 1.3.2 - Copyright INRIA - CeCILL License SYNOPSIS kissreads/kissreads <toCheck.fasta> <readsC1.fasta> [<readsC2.fasta> [<readsC3.fasta] ...] [-k value] [-c value] [-d 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. -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) -m align_file, write a file of reads mapped to sequences in file align_file -s silent mode --version get the kissReads version and exit -f outputs coherent events in a standard fasta file format -h prints this message and exit
The full documentation for kissreads is maintained as a Texinfo manual. If the info and kissreads programs are properly installed at your site, the command info kissreads should give you access to the complete manual.