RNA-seq-analysis by crazyhottommy

RNAseq analysis notes from Ming Tang

updated at May 8, 2024, 8:01 a.m.

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AGAT by NBISweden

Another Gtf/Gff Analysis Toolkit

updated at May 8, 2024, 6:40 a.m.

46 +0

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redun by insitro

Yet another redundant workflow engine

updated at May 8, 2024, 6:24 a.m.

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scipipe by scipipe

Robust, flexible and resource-efficient pipelines using Go and the commandline

updated at May 8, 2024, 1:20 a.m.

38 +0

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common-workflow-language by common-workflow-language

Repository for the CWL standards. Use https://cwl.discourse.group/ for support 😊

updated at May 7, 2024, 9:45 p.m.

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1,442 +1

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FastQC by s-andrews

A quality control analysis tool for high throughput sequencing data

updated at May 7, 2024, 1:45 p.m.

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seqan3 by seqan

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

updated at May 7, 2024, 9:11 a.m.

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parasail by jeffdaily

Pairwise Sequence Alignment Library

updated at May 7, 2024, 8:34 a.m.

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freebayes by freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

updated at May 7, 2024, 8:33 a.m.

46 +0

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seqkit by shenwei356

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

updated at May 6, 2024, 2:26 p.m.

27 +0

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oneliners by stephenturner

Useful bash one-liners for bioinformatics.

updated at May 6, 2024, 12:35 p.m.

157 +0

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ngs-preprocess by fmalmeida

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

updated at May 6, 2024, 6:36 a.m.

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vcflib by vcflib

C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings

updated at May 6, 2024, 3:45 a.m.

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bamtools by pezmaster31

C++ API & command-line toolkit for working with BAM data

updated at May 6, 2024, 3:08 a.m.

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RSEM by deweylab

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data

updated at May 5, 2024, 8:28 a.m.

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GLnexus by dnanexus-rnd

Scalable gVCF merging and joint variant calling for population sequencing projects

updated at May 5, 2024, 5:51 a.m.

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mosdepth by brentp

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

updated at May 3, 2024, 12:24 p.m.

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pysam by pysam-developers

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.

updated at May 3, 2024, 4:14 a.m.

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rnaseq_tutorial by griffithlab

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

updated at May 3, 2024, 2:10 a.m.

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somalier by brentp

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

updated at May 2, 2024, 2:45 p.m.

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