scipipe by scipipe

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

updated at May 20, 2024, 7:50 p.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 21, 2024, 9:40 a.m.

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bacannot by fmalmeida

Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.

updated at May 21, 2024, 9:50 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 21, 2024, 2:40 p.m.

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smoove by brentp

structural variant calling and genotyping with existing tools, but, smoothly.

updated at May 23, 2024, 1:39 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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cyvcf2 by brentp

cython + htslib == fast VCF and BCF processing

updated at May 25, 2024, 2:29 p.m.

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SnpEff by pcingola

None

updated at May 26, 2024, 3:09 a.m.

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jbrowse by GMOD

JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.

updated at May 26, 2024, 12:57 p.m.

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delly by dellytools

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

updated at May 26, 2024, 10:08 p.m.

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manta by Illumina

Structural variant and indel caller for mapped sequencing data

updated at May 26, 2024, 10:09 p.m.

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bioperl-live by bioperl

Core BioPerl 1.x code

updated at May 27, 2024, 12:55 a.m.

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octopus by luntergroup

Bayesian haplotype-based mutation calling

updated at May 27, 2024, 6:03 a.m.

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fujiplot by mkanai

Fuji plot—a circos representation of multiple GWAS results—

updated at May 27, 2024, 7:10 a.m.

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bamsurgeon by adamewing

tools for adding mutations to existing .bam files, used for testing mutation callers

updated at May 28, 2024, 9:52 a.m.

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freebayes by freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

updated at May 28, 2024, 10:48 a.m.

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wtdbg2 by ruanjue

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly

updated at May 28, 2024, 6:27 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 28, 2024, 9:11 p.m.

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vcfanno by brentp

annotate a VCF with other VCFs/BEDs/tabixed files

updated at May 29, 2024, 12:30 a.m.

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