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kmc - Online in the Cloud

Run kmc in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command kmc 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


kmc - count kmers in genomic sequences

DESCRIPTION


KMC—K-mer Counter is a utility designed for counting k-mers (sequences of consecutive k
symbols) in a set of reads from genome sequencing projects.

SYNOPSIS


kmc [options] <input_file_name> <output_file_name> <working_directory>

kmc [options] <@input_file_names> <output_file_name> <working_directory>

OPTIONS


-v - verbose mode (shows all parameter settings); default: false

-k<len> - k-mer length (k from 1 to 256; default: 25)

-m<size> - max amount of RAM in GB (from 1 to 1024); default: 12

-sm - use strict memory mode (memory limit from -m<n> switch will not be exceeded)

-p<par> - signature length (5, 6, 7, 8); default: 7

-f<a/q/m> - input in FASTA format (-fa), FASTQ format (-fq) or mulit FASTA (-fm); default:
FASTQ

-q[value] - use Quake's compatible counting with [value] representing lowest quality
(default: 33)

-ci<value> - exclude k-mers occurring less than <value> times (default: 2)

-cs<value> - maximal value of a counter (default: 255)

-cx<value> - exclude k-mers occurring more of than <value> times (default: 1e9)

-b - turn off transformation of k-mers into canonical form

-r - turn on RAM-only mode

-n<value> - number of bins

-t<value> - total number of threads (default: no. of CPU cores)

-sf<value> - number of FASTQ reading threads

-sp<value> - number of splitting threads

-sr<value> - number of sorter threads

-so<value> - number of threads per single sorter

EXAMPLES


kmc -k27 -m24 NA19238.fastq NA.res \data\kmc_tmp_dir\

kmc -k27 -q -m24 @files.lst NA.res \data\kmc_tmp_dir\

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