MetaCRAM

MetaCRAM is a specialized software suite for processing and compressing large metagenomic files. It integrates algorithms for taxonomy identification and assembly, and introduces parallel execution methods, genome reference selection and CRAM-based compression. It allows for fast selection of relevant files in the compressed domain and offers improved compression ratios compared to gzip. MetaCRAM is freely available and requires a minimum of 16 GB of RAM to run.

Topic

Metagenomics;Taxonomy;Sequencing

Detail

  • Operation: Sequence assembly;Taxonomic classification

  • Software interface: Command-line user interface

  • Language: Java;Perl

  • License: -

  • Cost: Free

  • Version name: -

  • Credit: National Science Foundation, National Institute of Health, the National Science Foundation Graduate Research Fellowship Program.

  • Input: -

  • Output: -

  • Contact: mkim158@illinois.edu;xzhan121@illinois.edu

  • Collection: -

  • Maturity: -

Publications

  • MetaCRAM: an integrated pipeline for metagenomic taxonomy identification and compression.
  • Kim M, et al. MetaCRAM: an integrated pipeline for metagenomic taxonomy identification and compression. MetaCRAM: an integrated pipeline for metagenomic taxonomy identification and compression. 2016; 17:94. doi: 10.1186/s12859-016-0932-x
  • https://doi.org/10.1186/s12859-016-0932-x
  • PMID: 26895947
  • PMC: PMC4759986

Download and documentation

    Currently not available or not maintained.

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