deepvariant by google

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

updated at May 23, 2024, 1:24 p.m.

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hifiasm by chhylp123

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

updated at May 23, 2024, 1:39 p.m.

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mosdepth by brentp

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

updated at May 23, 2024, 3:09 p.m.

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freebayes by freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

updated at May 23, 2024, 3:11 p.m.

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FastQC by s-andrews

A quality control analysis tool for high throughput sequencing data

updated at May 23, 2024, 4:03 p.m.

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MMseqs2 by soedinglab

MMseqs2: ultra fast and sensitive search and clustering suite

updated at May 23, 2024, 7:04 p.m.

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vcftools by vcftools

A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.

updated at May 24, 2024, 12:47 a.m.

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wgsim by lh3

Reads simulator

updated at May 24, 2024, 1:36 a.m.

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zindex by mattgodbolt

Create an index on a compressed text file

updated at May 24, 2024, 3:50 a.m.

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nextflow by nextflow-io

A DSL for data-driven computational pipelines

updated at May 24, 2024, 4:17 a.m.

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bowtie2 by BenLangmead

A fast and sensitive gapped read aligner

updated at May 24, 2024, 7:19 a.m.

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AfterQC by OpenGene

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

updated at May 24, 2024, 7:31 a.m.

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ngs-preprocess by fmalmeida

A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies

updated at May 24, 2024, 8:04 a.m.

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AGAT by NBISweden

Another Gtf/Gff Analysis Toolkit

updated at May 24, 2024, 8:17 a.m.

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samtools by samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

updated at May 24, 2024, 9:30 a.m.

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bwa by lh3

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

updated at May 24, 2024, 10:30 a.m.

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seqkit by shenwei356

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation

updated at May 24, 2024, 12:05 p.m.

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Flye by fenderglass

De novo assembler for single molecule sequencing reads using repeat graphs

updated at May 24, 2024, 1:43 p.m.

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genozip by divonlan

A modern compressor for genomic files (FASTQ, SAM/BAM/CRAM, VCF, FASTA, GFF/GTF/GVF, 23andMe...), up to 5x better than gzip and faster too

updated at May 24, 2024, 2 p.m.

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bpipe by ssadedin

Bpipe - a tool for running and managing bioinformatics pipelines

updated at May 24, 2024, 2:14 p.m.

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