NAME
ntcard - Streaming algorithm to estimate cardinality in genomics datasets
SYNOPSIS
ntCard [OPTION]... FILE(S)...
DESCRIPTION
Estimates k-mer coverage histogram in FILE(S).
Acceptable file formats: fastq, fasta, sam, bam and in compressed formats gz, bz, zip, xz. A list of files containing file names in each row can be passed with @ prefix.
-
Options:
- -t, --threads=N
-
use N parallel threads [1] (N>=2 should be used when input files are >=2)
- -k, --kmer=N
-
the length of kmer
- -g, --gap=N
-
the length of gap in the gap seed [0]. g mod 2 must equal k mod 2 unless g == 0 -g does not support multiple k currently.
- -c, --cov=N
-
the maximum coverage of kmer in output [1000]
- -p, --pref=STRING
-
the prefix for output file name(s)
- -o, --output=STRING
-
the name for output file name (used when output should be a single file)
- --help
-
display this help and exit
--version output version information and exit
REPORTING BUGS
Report bugs to https://github.com/bcgsc/ntCard/issues
AUTHOR
This manpage was written by Nilesh Patra for the Debian distribution and
can be used for any other usage of the program.