Description

Efficiently counts k-mers from DNA sequencing reads using a fast, memory-efficient, parallelized algorithm

Input

Name
Description
Pattern

0 ()

1 ()

kmer_length (integer)

k-mer size to use

size (string)

Specifies the memory hash size (in bytes) to allocate for the k-mer counting hash table (e.g., '100M'). A mean estimation could be carried with this formula: 'genome size + (genome size coverage kmer-length * error rate)'

Output

Name
Description
Pattern

0 ()

0 ()

Tools

jellyfish Documentation

Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence

https://github.com/gmarcais/Jellyfishdoi: 10.1093/bioinformatics/btr011License: GPL v3
Authors