Abstract
The IMG Annotation Pipeline is a collection of Bash and Python scripts to control a workflow for structural and functional annotation of prokaryotic genomes, metagenomes, and metatranscriptomes. The bash scripts in general control the overall workflow and are wrappers around 3rd party executables (not included in repo) that predict features or functions. Whereas the Python scripts do post-processing of raw output in terms of filtering or format transformation and in some cases contain some logic for picking the correct predictions or resolving overlaps. The pipeline is tailored to produce results required by IMG (https://img.jgi.doe.gov/) and is executed on every dataset submitted to IMG via https://img.jgi.doe.gov/submit. These consist of internal genomes, metagenomes and metatranscriptomes sequenced and assembled at the JGI, as well as datasets submitted by external users (non-lab/JGI affiliates).
- Developers:
-
Huntemann, Marcel [1] ; Ivanova, Natalia [1]
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Release Date:
- 2023-03-30
- Project Type:
- Open Source, Publicly Available Repository
- Software Type:
- Scientific
- Licenses:
-
GNU General Public License v3.0
- Sponsoring Org.:
-
USDOEPrimary Award/Contract Number:AC02-05CH11231
- Code ID:
- 134858
- Site Accession Number:
- 2023-053
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Country of Origin:
- United States
Citation Formats
Huntemann, Marcel, and Ivanova, Natalia.
IMG Annotation Pipeline (IMGAP) v5.1.13.
Computer Software.
https://code.jgi.doe.gov/img/img-pipelines/img-annotation-pipeline.
USDOE.
30 Mar. 2023.
Web.
doi:10.11578/dc.20240716.3.
Huntemann, Marcel, & Ivanova, Natalia.
(2023, March 30).
IMG Annotation Pipeline (IMGAP) v5.1.13.
[Computer software].
https://code.jgi.doe.gov/img/img-pipelines/img-annotation-pipeline.
https://doi.org/10.11578/dc.20240716.3.
Huntemann, Marcel, and Ivanova, Natalia.
"IMG Annotation Pipeline (IMGAP) v5.1.13." Computer software.
March 30, 2023.
https://code.jgi.doe.gov/img/img-pipelines/img-annotation-pipeline.
https://doi.org/10.11578/dc.20240716.3.
@misc{
doecode_134858,
title = {IMG Annotation Pipeline (IMGAP) v5.1.13},
author = {Huntemann, Marcel and Ivanova, Natalia},
abstractNote = {The IMG Annotation Pipeline is a collection of Bash and Python scripts to control a workflow for structural and functional annotation of prokaryotic genomes, metagenomes, and metatranscriptomes. The bash scripts in general control the overall workflow and are wrappers around 3rd party executables (not included in repo) that predict features or functions. Whereas the Python scripts do post-processing of raw output in terms of filtering or format transformation and in some cases contain some logic for picking the correct predictions or resolving overlaps. The pipeline is tailored to produce results required by IMG (https://img.jgi.doe.gov/) and is executed on every dataset submitted to IMG via https://img.jgi.doe.gov/submit. These consist of internal genomes, metagenomes and metatranscriptomes sequenced and assembled at the JGI, as well as datasets submitted by external users (non-lab/JGI affiliates).},
doi = {10.11578/dc.20240716.3},
url = {https://doi.org/10.11578/dc.20240716.3},
howpublished = {[Computer Software] \url{https://doi.org/10.11578/dc.20240716.3}},
year = {2023},
month = {mar}
}