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About 10,000 papers for “Contig”

Contig

National Human Genome Research Institute (NHGRI) · Definitions · 2019

A contig--from the word "contiguous"--is a series of overlapping DNA sequences used to make a physical map that reconstructs the original DNA sequence of a chromosome or a region of a chromosome.A contig can also refer to one of the DNA sequences used in making such a map.

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Contig

Hawley's Condensed Chemical Dictionary · 2007

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Contig

National Cancer Institute · Definitions · 2020

created by assembling these overlapping chromosome fragments.

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contig assembly

Iskandar Zulkarnaen Siregar, Rahadian Pratama, Deden Derajat Matra et al. · Figshare · 2020

corrected contig assemblies of ebony from two assembler, Canu and SMARTdenovo

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contig assembly

Siregar, Iskandar Zulkarnaen, Rahadian Pratama, Deden Derajat Matra et al. · Figshare · 2020

corrected contig assemblies of ebony from two assembler, Canu and SMARTdenovo

Cited by 1Open access

Contig Coverage

Calla Martyn · Figshare · 2022

Coverage summary statistics of represenative contigs for each tick sample.

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Haplotype contig

The Dictionary of Genomics, Transcriptomics and Proteomics · 2015

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contig-tools

Underwood, Anthony · Zenodo (CERN European Organization for Nuclear Research) · 2022

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 &lt;COMMAND&gt; -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 &gt; 500bp Total length %GC Largest contig N50 score conditions that can be used are gt =&gt; greater than lt =&gt; less than lt_gt =&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>&gt;gene1 GCAGCTAGCGACTGCGAC..... &gt;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 &lt;NUMBER PARALLEL PROCESSES&gt;</code>. If you only want to write out genomes where the queries are co-located use the <code>-y</code> options

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Contig Clustering

Martyn, Calla · Figshare · 2022

CD-HIT clustering of all dataset contigs at 85% nucleotide identity

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Mini‐contig

The Dictionary of Genomics, Transcriptomics and Proteomics · 2015

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Contig Clustering

Calla Martyn · Figshare · 2022

CD-HIT clustering of all dataset contigs at 85% nucleotide identity

Cited by 0Open access

Contig Coverage

Martyn, Calla · Figshare · 2022

Coverage summary statistics of represenative contigs for each tick sample.

Cited by 0Open access