test_all

count k-mers in DNA sequences (examples for testing)

Install

All systems
curl cmd.cat/test_all.sh
Debian Debian
apt-get install jellyfish-examples
Ubuntu
apt-get install jellyfish-examples
image/svg+xml Kali Linux
apt-get install jellyfish-examples
Windows (WSL2)
sudo apt-get update sudo apt-get install jellyfish-examples
Dockerfile
dockerfile.run/test_all

jellyfish-examples

count k-mers in DNA sequences (examples for testing)

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 using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages 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. This package contains examples to test the package