title: The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4).
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.
authors.affiliation: Genome Biology Program, Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut, Creek USA.
authors.forename: Marcel
authors.initials: M
authors.lastname: Huntemann
authors.affiliation: Genome Biology Program, Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut, Creek USA.
authors.forename: Natalia N
authors.initials: NN
authors.lastname: Ivanova
authors.affiliation: Genome Biology Program, Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut, Creek USA.
authors.forename: Konstantinos
authors.initials: K
authors.lastname: Mavromatis
authors.affiliation: Genome Biology Program, Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut, Creek USA.
authors.forename: H James
authors.initials: HJ
authors.lastname: Tripp
authors.affiliation: Genome Biology Program, Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut, Creek USA.
authors.forename: David
authors.initials: D
authors.lastname: Paez-Espino
authors.affiliation: Genome Biology Program, Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut, Creek USA.
authors.forename: Kristin
authors.initials: K
authors.lastname: Tennessen
authors.affiliation: Biosciences Computing, Computational Research Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, USA.
authors.forename: Krishnaveni
authors.initials: K
authors.lastname: Palaniappan
authors.affiliation: Biosciences Computing, Computational Research Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, USA.
authors.forename: Ernest
authors.initials: E
authors.lastname: Szeto
authors.affiliation: Biosciences Computing, Computational Research Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, USA.
authors.forename: Manoj
authors.initials: M
authors.lastname: Pillay
authors.affiliation: Biosciences Computing, Computational Research Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, USA.
authors.forename: I-Min A
authors.initials: IM
authors.lastname: Chen
authors.affiliation: Genome Biology Program, Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut, Creek USA.
authors.forename: Amrita
authors.initials: A
authors.lastname: Pati
authors.affiliation: Genome Biology Program, Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut, Creek USA.
authors.forename: Torben
authors.initials: T
authors.lastname: Nielsen
authors.affiliation: Biosciences Computing, Computational Research Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, USA.
authors.forename: Victor M
authors.initials: VM
authors.lastname: Markowitz
authors.affiliation: Genome Biology Program, Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut, Creek USA.
authors.forename: Nikos C
authors.initials: NC
authors.lastname: Kyrpides
keywords: IMG; JGI; Metagenome annotation; SOP