The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4)

Huntemann, Marcel; Ivanova, Natalia N.; Mavromatis, Konstantinos; Tripp, H. James; Paez-Espino, David; Tennessen, Kristin; Palaniappan, Krishnaveni; Szeto, Ernest; Pillay, Manoj; Chen, I-Min A.; Pati, Amrita; Nielsen, Torben; Markowitz, Victor M.; Kyrpides, Nikos C.

doi:10.1186/s40793-016-0138-x

The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4)

Journal Article · Tue Feb 23 23:00:00 EST 2016 · Standards in Genomic Sciences

DOI:https://doi.org/10.1186/s40793-016-0138-x· OSTI ID:1618964

Huntemann, Marcel; Ivanova, Natalia N.; Mavromatis, Konstantinos; Tripp, H. James; Paez-Espino, David; Tennessen, Kristin; Palaniappan, Krishnaveni; Szeto, Ernest; Pillay, Manoj; Chen, I-Min A.; Pati, Amrita; Nielsen, Torben; Markowitz, Victor M.; Kyrpides, Nikos C.

Abstract

The DOE-JGI Metagenome Annotation Pipeline (MAP v.4) performs structural and functional annotation for metagenomic sequences that are submitted to the Integrated Microbial Genomes with Microbiomes (IMG/M) system for comparative analysis. The pipeline runs on nucleotide sequences provided via the IMG submission site. Users must first define their analysis projects in GOLD and then submit the associated sequence datasets consisting of scaffolds/contigs with optional coverage information and/or unassembled reads in fasta and fastq file formats. The MAP processing consists of feature prediction including identification of protein-coding genes, non-coding RNAs and regulatory RNAs, as well as CRISPR elements. Structural annotation is followed by functional annotation including assignment of protein product names and connection to various protein family databases.

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Sponsoring Organization:: USDOE

Grant/Contract Number:: NONE; AC02-05CH11231

OSTI ID:: 1618964

Alternate ID(s):: OSTI ID: 1379106

Journal Information:: Standards in Genomic Sciences, Journal Name: Standards in Genomic Sciences Journal Issue: 1 Vol. 11; ISSN 1944-3277

Publisher:: Springer Science + Business MediaCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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