KMC_TOOLS(1) | KMC_TOOLS(1) |
NAME¶
kmc_tools - additional operations on k-mer databasesSYNOPSIS¶
kmc_tools [global parameters] <operation> [operation parameters]DESCRIPTION¶
This command and its various subcomments implement a number of operations on KMC databases.k-mers sets operations for 2 KMC databases¶
intersectintersection of 2 k-mers sets
kmers_subtract
subtraction of 2 k-mers sets
counters_subtract
counters subtraction of 2 k-mer sets
union
union of 2 k-mers sets
operations for single kmc database¶
sortsorts k-mers from database generated by KMC2.x
reduce
exclude too rare and too frequent k-mers
compact
remove counters (store only k-mers)
histogram
histogram of k-mers occurr ences
dump
dump k-mers and counters to text file
more complex operations:¶
complexcomplex operations with a number of input databases
other operations:¶
filterfilter out reads with too small number of k-mers
OPTIONS¶
global parameters:¶
-t<value>total number of threads (default: no. of CPU cores)
-v
enable verbose mode (shows some information) (default:
false)
-hp
hide percentage progress (default: false)
EXAMPLE¶
kmc_tools union db1 -ci3 db2 -ci5 -cx300 db1_union_db2 -ci10SEE ALSO¶
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)AUTHOR¶
KMC was originally written by:•Sebastian Deorowicz (
•Marek Kokot
•Szymon Grabowski
•Agnieszka Debudaj-Grabysz