jellyfish-examples_2.1.4-1_amd64.deb


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Description

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

Distribution: Debian 8 (Jessie)
Repository: Debian Main amd64
Package name: jellyfish-examples
Package version: 2.1.4
Package release: 1
Package architecture: amd64
Package type: deb
Installed size: 1.89 KB
Download size: 452.17 KB
Official Mirror: ftp.br.debian.org
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

Alternatives

    Download

    Source package: jellyfish

    Install Howto

    1. Update the package index:
      # sudo apt-get update
    2. Install jellyfish-examples deb package:
      # sudo apt-get install jellyfish-examples

    Files

    • /usr/lib/jellyfish/bin/generate_sequence
    • /usr/lib/jellyfish/bin/jellyfish
    • /usr/lib/jellyfish/bin/test_all
    • /usr/share/doc/jellyfish-examples/changelog.Debian.gz
    • /usr/share/doc/jellyfish-examples/changelog.gz
    • /usr/share/doc/jellyfish-examples/copyright
    • /usr/share/doc/jellyfish-examples/examples/big.sh
    • /usr/share/doc/jellyfish-examples/examples/bloom_counter.sh
    • /usr/share/doc/jellyfish-examples/examples/bloom_filter.sh
    • /usr/share/doc/jellyfish-examples/examples/compat.sh
    • /usr/share/doc/jellyfish-examples/examples/compat.sh.in
    • /usr/share/doc/jellyfish-examples/examples/from_stream.sh
    • /usr/share/doc/jellyfish-examples/examples/from_stream_fastq.sh
    • /usr/share/doc/jellyfish-examples/examples/generate_fastq_sequence.sh
    • /usr/share/doc/jellyfish-examples/examples/generate_sequence.sh
    • /usr/share/doc/jellyfish-examples/examples/large_key.sh
    • /usr/share/doc/jellyfish-examples/examples/merge.sh
    • /usr/share/doc/jellyfish-examples/examples/min_qual.sh
    • /usr/share/doc/jellyfish-examples/examples/multi_file.sh
    • /usr/share/doc/jellyfish-examples/examples/multi_file_fastq.sh
    • /usr/share/doc/jellyfish-examples/examples/parallel_direct_indexing.sh
    • /usr/share/doc/jellyfish-examples/examples/parallel_fastq_direct_indexing.sh
    • /usr/share/doc/jellyfish-examples/examples/parallel_fastq_hashing.sh
    • /usr/share/doc/jellyfish-examples/examples/parallel_fastq_sequence_hashing.sh
    • /usr/share/doc/jellyfish-examples/examples/parallel_hashing.sh
    • /usr/share/doc/jellyfish-examples/examples/parsers.sh
    • /usr/share/doc/jellyfish-examples/examples/quality_filter.sh
    • /usr/share/doc/jellyfish-examples/examples/raw_hash.sh
    • /usr/share/doc/jellyfish-examples/examples/serial_direct_indexing.sh
    • /usr/share/doc/jellyfish-examples/examples/serial_hashing.sh
    • /usr/share/doc/jellyfish-examples/examples/small.sh
    • /usr/share/doc/jellyfish-examples/examples/subset_hashing.sh
    • /usr/share/doc/jellyfish-examples/examples/unit_tests.sh

    Changelog

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