other · Zenodo (CERN European Organization for Nuclear Research) · 2022
contig-tools
Underwood, Anthony
Cited by 0Open access
Abstract
Contig Tools Installation <pre><code>pip3 install contig-tools</code></pre> source code: https://gitlab.com/antunderwood/contig_tools Usage <pre><code>usage: contig-tools [-h] [-v] {filter,metrics,check_metrics,co_located} ... A package to maniuplate and assess contigs arising from de novo assemblies positional arguments: {filter,metrics,check_metrics,co_located} The following commands are available. Type contig_tools <COMMAND> -h for more help on a specific commands filter Filter contigs based on either length and/or coverage metrics Print contig metrics check_metrics check contig metrics co_located check to see if two or more loci are found on the same contig. optional arguments: -h, --help show this help message and exit -v, --version display the version number</code></pre> Examples filter contigs <pre><code>contig-tools filter -l 500 -c 3 -f contigs.fasta</code></pre> print contig metrics <pre><code>contig-tools metrics -f contig_tools/tests/test_data/contigs_for_checks.fas contig-tools metrics -f contig_tools/tests/test_data/contigs_for_checks.fas -o json</code></pre> check if contigs meet conditions based on conditions enoded in a yaml file example yaml file <pre><code>N50 score: condition_type: gt condition_value: 10 Largest contig: condition_type: gt condition_value: 15 Total length: condition_type: lt_gt condition_value: - 100 - 50</code></pre> example command <pre><code>contig-tools check_metrics -f contigs.fasta -y conditions.yml</code></pre> metrics that can be checked are Number of contigs Number of contigs > 500bp Total length %GC Largest contig N50 score conditions that can be used are gt => greater than lt => less than lt_gt => less than and greater than check if a two or more loci are co-located Make a fasta query file with the 2 or more loci you want to see if they are co-located e.g <pre><code>>gene1 GCAGCTAGCGACTGCGAC..... >gene2 CTACGTAGGACACGACTA....</code></pre> There are two options Search a single genome file for the co-location of loci <pre><code>contig-tools co_located -q queries.fas -f /path/to/single/genome/contigs.fas</code></pre> or Search a list of genomes for the co-location of loci Make a text file with paths to genomes e.g <pre><code>/path/to/single/genome1.fas /path/to/single/genome1.fas ....</code></pre> and then run the command <pre><code>contig-tools co_located -q queries.fas -l /path/to/single/genome_list_file.txt</code></pre> If you have muliple cores on the computer you are running this on you can process the search in parallel using the <code>-n <NUMBER PARALLEL PROCESSES></code>. If you only want to write out genomes where the queries are co-located use the <code>-y</code> options
Cite this paper
Underwood, A. (2022). contig-tools. Zenodo (CERN European Organization for Nuclear Research). https://doi.org/10.5281/zenodo.6790356
Underwood, Anthony. “contig-tools.” Zenodo (CERN European Organization for Nuclear Research), 2022, https://doi.org/10.5281/zenodo.6790356.
Underwood, Anthony. 2022. “contig-tools.” Zenodo (CERN European Organization for Nuclear Research). https://doi.org/10.5281/zenodo.6790356.
Underwood, A. (2022) ‘contig-tools’, Zenodo (CERN European Organization for Nuclear Research). Available at: https://doi.org/10.5281/zenodo.6790356.
@misc{underwood2022contig,
title = {{contig-tools}},
author = {Underwood, Anthony},
journal = {Zenodo (CERN European Organization for Nuclear Research)},
year = {2022},
doi = {10.5281/zenodo.6790356}
}Made from the index record. Check names, capitalisation and page numbers against the paper. Need another style? AI for Research has over 10,000.