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awesome-bioinformatics

A curated list of awesome Bioinformatics libraries and software.

biobakery

bioBakery tools for meta'omic profiling

bowtie

An ultrafast memory-efficient short read aligner

challenges-francois

dmr-analysis

DMRcate Tim Peters

forestqc

Quality control on genetic variants from next-generation sequencing data using random forest

gatk4-rnaseq-germline-snps-indels

Workflows for processing RNA data for germline short variant discovery with GATK v4 and related tools

kneaddata

Quality control tool on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.

kraken2

The second version of the Kraken taxonomic sequence classification system

kraken2-output-manipulation

Kraken output generates a report for each datasets, this script takes these individual output and combines it to one file, where each column is number of reads that were rooted to this taxon (column 2 in summary)

lollipops

This is the development fork - Stable code has been moved to ==>

long-rna-seq-pipeline

STAR based ENCODE Long RNA-Seq processing pipeline

meffil

Efficient algorithms for analyzing DNA methylation data.

metaboanalystr

R package for MetaboAnalyst

mgnify-ebi-2020

mgnifyr

R package for searching, downloading and analysis of EBI MGnify metagenomics data

microbiomebestpracticereview

Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing

multiphate2

multiPhATE with comparative genomics

mutplot

ngs-pipe

NGS-pipe: next-generation sequencing pipelines for precision oncology

pipeline-structural-variation

Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data

samtools

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

sankeyplot

Sankey Plot script from davidsjoberg github

spoon-knife

This repo is for demonstration purposes only.

testfile

Generating pipeline to analyse test data set

vcfr

Tools to work with variant call format files

workshop_april

Git class