CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data
Creators
- 1. The University of Sydney
- 2. Technical University of Denmark
- 3. The Peter Doherty Institute for Infection and Immunity
Description
CCMetagen is a software to identify taxa from metagenome data. This repository contains CCMetagen version 1.0.0, which was benchmarked with other software in the original CCMetagen publication.
High-throughput sequencing of DNA and RNA from environmental and host-associated samples (metagenomics and metatranscriptomics) is a powerful tool to assess which organisms are present in a sample. Taxonomic identification software usually align individual short sequence reads to a reference database, sometimes containing taxa with complete genomes only. This is a challenging task given that different species can share identical sequence regions and complete genome sequences are only available for a fraction of organisms. A recently developed approach to map sequence reads to reference databases involves weighing all high scoring read-mappings to the data base as a whole to produce better-informed alignments. We used this novel concept in read mapping to develop a highly accurate metagenomic classification pipeline named CCMetagen. Our pipeline substantially outperforms other commonly used software in identifying bacteria and fungi, and can efficiently use the entire NCBI nucleotide collection as a reference to detect species with incomplete genome data from all biological kingdoms. CCMetagen is user-friendly and the results can be easily integrated into microbial community analysis software for streamlined and automated microbiome studies.
Files
CCMetagen-1.0.0.zip
Files
(645.4 kB)
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Additional details
Related works
- Is documented by
- Preprint: 10.1101/641332 (DOI)