Name: ntCard
Owner: BC Cancer Agency Canada's Michael Smith Genome Sciences Centre
Description: Estimating k-mer coverage histogram of genomics data
Created: 2016-05-30 23:15:42.0
Updated: 2017-12-14 14:40:41.0
Pushed: 2017-11-28 22:16:46.0
Homepage: http://www.bcgsc.ca/platform/bioinfo/software/ntcard
Size: 454
Language: C++
GitHub Committers
| User | Most Recent Commit | # Commits |
|---|---|---|
| Shaun Jackman | 2018-03-01 23:31:19.0 | 1 |
| Hamid Mohamadi | 2018-01-29 15:54:39.0 | 76 |
| Golnaz Jahesh | 2016-06-16 02:44:13.0 | 2 |
Other Committers
| User | Most Recent Commit | # Commits |
|---|
ntCard is a streaming algorithm for cardinality estimation in genomics datasets. As input it takes file(s) in fasta, fastq, sam, or bam formats and computes the total number of distinct k-mers, F0, and also the k-mer coverage frequency histogram, fi, i>=1.
Install Homebrew, and run the command
brew install homebrew/science/ntcard
When installing ntCard from GitHub source the following tools are required:
To generate the configure script and make files:
./autogen.sh
To compile and install ntCard in /usr/local:
configure
ke
do make install
To install ntCard in a specified directory:
configure --prefix=/opt/ntCard
ke
ke install
ntCard uses OpenMP for parallelization, which requires a modern compiler such as GCC 4.2 or greater. If you have an older compiler, it is best to upgrade your compiler if possible. If you have multiple versions of GCC installed, you can specify a different compiler:
configure CC=gcc-xx CXX=g++-xx
For the best performance of ntCard, pass -O3 flag:
configure CFLAGS='-g -O3' CXXFLAGS='-g -O3'
To run ntCard, its executables should be found in your PATH. If you installed ntCard in /opt/ntCard, add /opt/ntCard/bin to your PATH:
TH=/opt/ntCard/bin:$PATH
rd [OPTIONS] ... [FILE]
Parameters:
-k, --kmer=SIZE: the length of k-mer [64]-t, --threads=N: use N parallel threads [1]-c, --cov=N: the maximum coverage of k-mer in output [64]-p, --pref=STRING: the prefix for output file name [freq]FILE: input file or set of files seperated by space, in fasta, fastq, sam, and bam formats. The files can also be in compressed (.gz, .bz2, .xz) formats . A list of files containing file names in each row can be passed with @ prefix.For example to run ntcard on a test file reads.fastq with k=50:
card -k50 reads.fastq
To run ntcard on a test file reads.fastq with multiple k's k=32,64,96,128 use:
card -k32,64,96,128 reads.fastq
As another example, to run ntcard on 5 input files file_1.fq.gz, file_2.fa, file_3.sam, file_4.bam, file_5.fq with k=64 and 6 threads and maximum output of frequencies c=100:
card -k64 -c100 -t6 file_1.fq.gz file_2.fa file_3.sam file_4.bam file_5.fq
If we have a list of input files lib.in with input file names in each row and want to run ntCard with k=144 and 12 threads:
card -k144 -t12 @lib.in
Hamid Mohamadi, Hamza Khan, and Inanc Birol. ntCard: a streaming algorithm for cardinality estimation in genomics data. Bioinformatics (2017) 33 (9): 1324-1330. 10.1093/bioinformatics/btw832