'\" t
.\"     Title: kmc_tools
.\"    Author: [see the "AUTHOR(S)" section]
.\" Generator: Asciidoctor 2.0.18
.\"      Date: 
.\"    Manual: \ \&
.\"    Source: \ \&
.\"  Language: English
.\"
.TH "KMC_TOOLS" "1" "" "\ \&" "\ \&"
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.SH "NAME"
kmc_tools \- additional operations on k\-mer databases
.SH "SYNOPSIS"
.sp
\fBkmc_tools\fP [global parameters] <operation> [operation parameters]
.SH "DESCRIPTION"
.sp
This command and its various subcomments implement a number of operations on
KMC databases.
.SS "k\-mers sets operations for 2 KMC databases"
.sp
\fBintersect\fP
.RS 4
intersection of 2 k\-mers sets
.RE
.sp
\fBkmers_subtract\fP
.RS 4
subtraction of 2 k\-mers sets
.RE
.sp
\fBcounters_subtract\fP
.RS 4
counters subtraction of 2 k\-mer sets
.RE
.sp
\fBunion\fP
.RS 4
union of 2 k\-mers sets
.RE
.SS "operations for single kmc database"
.sp
\fBsort\fP
.RS 4
sorts k\-mers from database generated by KMC2.x
.RE
.sp
\fBreduce\fP
.RS 4
exclude too rare and too frequent k\-mers
.RE
.sp
\fBcompact\fP
.RS 4
remove counters (store only k\-mers)
.RE
.sp
\fBhistogram\fP
.RS 4
histogram of k\-mers occurr ences
.RE
.sp
\fBdump\fP
.RS 4
dump k\-mers and counters to text file
.RE
.SS "more complex operations:"
.sp
\fBcomplex\fP
.RS 4
complex operations with a number of input databases
.RE
.SS "other operations:"
.sp
\fBfilter\fP
.RS 4
filter out reads with too small number of k\-mers
.RE
.SH "OPTIONS"
.SS "global parameters:"
.sp
\fB\-t<value>\fP
.RS 4
total number of threads (default: no. of CPU cores)
.RE
.sp
\fB\-v\fP
.RS 4
enable verbose mode (shows some information) (default: false)
.RE
.sp
\fB\-hp\fP
.RS 4
hide percentage progress (default: false)
.RE
.SH "EXAMPLE"
.sp
kmc_tools union db1 \-ci3 db2 \-ci5 \-cx300 db1_union_db2 \-ci10
.SH "SEE ALSO"
.sp
kmc(1), kmc_tools\-histogram(1), kmc_tools\-compact(1), kmc_tools\-intersect(1),
kmc_tools\-complex(1), kmc_tools\-kmers_subtract(1), kmc_tools\-counters_subtract(1),
kmc_tools\-sort(1), kmc_tools\-dump(1), kmc_tools\-union(1), kmc_tools\-filter(1)
.SH "AUTHOR"
.sp
KMC was originally written by:
.sp
.RS 4
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Sebastian Deorowicz (\c
.MTO "sebastian.deorowicz\(atpolsl.pl" "" ")"
.RE
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.RS 4
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Marek Kokot
.RE
.sp
.RS 4
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Szymon Grabowski
.RE
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.RS 4
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Agnieszka Debudaj\-Grabysz
.RE
.SH "COPYING"
.sp
KMC is free software distributed under GNU GPL3 licence for academic,
research, and commercial use.