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Read depth analysis software tools | Whole-genome sequencing

The theoretical or expected coverage is the average number of times that each nucleotide is expected to be sequenced given a certain number of reads of a given length and the assumption that reads are randomly distributed across an idealized…
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SAMtools
Desktop

SAMtools

A suite of programs for interacting with high-throughput sequencing data. It…

A suite of programs for interacting with high-throughput sequencing data. It can manipulate alignments in the SAM/BAM/CRAM formats : reading, writing, editing, indexing, viewing and converting…

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BEDTools
Desktop

BEDTools

A software suite for the comparison, manipulation and annotation of genomic…

A software suite for the comparison, manipulation and annotation of genomic features in browser extensible data (BED) and general feature format (GFF) format. BEDTools also supports the comparison of…

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GATK-Queue
Desktop

GATK-Queue Genome Analysis Toolkit-Queue

A command-line scripting framework for defining multi-stage genomic analysis…

A command-line scripting framework for defining multi-stage genomic analysis pipelines combined with an execution manager that runs those pipelines from end-to-end. Often processing genome data…

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GATK
Desktop

GATK Genome Analysis ToolKit

Focuses on variant discovery and genotyping. GATK provides a toolkit, developed…

Focuses on variant discovery and genotyping. GATK provides a toolkit, developed at the Broad Institute, composed of several tools and ables to support projects of any size. The application compiles…

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Sambamba
Desktop

Sambamba

A high performance robust tool and library for working with SAM, BAM and CRAM…

A high performance robust tool and library for working with SAM, BAM and CRAM sequence alignment files; the most common file formats for aligned next generation sequencing (NGS) data. Sambamba is a…

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COV2HTML
Web

COV2HTML

An interactive web interface addressed to biologists, allowing both coverage…

An interactive web interface addressed to biologists, allowing both coverage visualization and analysis of NGS alignments performed on prokaryotic organisms (bacteria and phages). Its strength is to…

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mosdepth
Desktop

mosdepth

Permits exome, whole-genome, and targeted sequencing analyses. Mosdepth is a…

Permits exome, whole-genome, and targeted sequencing analyses. Mosdepth is a convenient application for genome-wide depth calculation that tracks chunks of read alignments. While the method it…

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Goleft
Desktop

Goleft

Enables coverage profiling at low computational cost, provides an interactive…

Enables coverage profiling at low computational cost, provides an interactive output that facilitates the detection of coverage anomalies (deletions, duplications, sex chromosome anomalies). Goleft…

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BadRegionFinder
Desktop

BadRegionFinder

Identifies regions with a bad, acceptable and good coverage in sequence…

Identifies regions with a bad, acceptable and good coverage in sequence alignment data available as bam files. BadRegionFinder offers various visual and textual types of output. The whole genome may…

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BpMatch
Desktop

BpMatch

A statistical method to analyse genomic sequences. BpMatch computes the…

A statistical method to analyse genomic sequences. BpMatch computes the coverage of a source sequence S on a target sequence T, by taking into account direct and reverse segments, eventually…

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CoverageCalcula…
Desktop

CoverageCalculator

Small and very fast utility to calculate X-coverage from…

Small and very fast utility to calculate X-coverage from Next-Generation-Sequencing data.

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