Revision 434dcb7ff9b0faf859f658de5c016192eb91b6e3 authored by Hamid Mohamadi on 31 October 2016, 20:40:58 UTC, committed by GitHub on 31 October 2016, 20:40:58 UTC
1 parent 76cef0a
README.md
ntCard
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ntCard is a streaming algorithm for cardinality estimation in genomics datasets. As iput it takes file(s) is fastq, fastq, sam, or bam formats and computes the total number of distinct k-mers, *F<sub>0</sub>*, and also the *k*-mer coverage frequency histogram, *f<sub>i</sub>*, *i>=1*.
# Build the binary for ntcard
Run:
```
$ make
```
# Run ntcard
```
ntcard [OPTIONS] ... [FILE]
```
Parameters:
* `-k`, `--kmer=SIZE`: the length of *k*-mer used for runtime test hashing `[64]`
* `-t`, `--threads=N`: use N parallel threads `[1]`
* `-c`, `--cov=N`: the maximum coverage of kmer in output `[64]`
* `FILE`: is the input file or set of files sepreted by space in fasta, fastq, sam, bam formats. The files can also be in compressed (`.gz`, `.bz2`, `.xz`) formats . A list of files containing file names in each rows can be passe with `@` prefix.
For example to run ntcard on a test file `reads.fastq` with `k=50`:
```
$ ntcard -k50 reads.fastq
```
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