13 lines
669 B
Plaintext
13 lines
669 B
Plaintext
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.
|
|
Jellyfish can count k-mers quickly by using an efficient encoding of a
|
|
hash table and by exploiting the "compare-and-swap" CPU instruction to
|
|
increase parallelism.
|
|
|
|
Jellyfish is a command-line program that reads FASTA and multi-FASTA
|
|
files containing DNA sequences. It outputs its k-mer counts in an binary
|
|
format, which can be translated into a human-readable text format using
|
|
the "jellyfish dump" command. See the documentation below for more
|
|
details.
|