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awesome-bioinfo-tools

A curated list of awesome Bioinformatics tools.
https://github.com/RipollJ/awesome-bioinfo-tools

Last synced: 4 days ago
JSON representation

  • Suite tools

    • samtools
    • EA-Utils - line tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc. Primarily written to support an Illumina based pipeline - but should work with any FASTQs.
    • BBtools
    • GATK

  • Quality analysis & trimming tools

    • trimming

      • Sickle
      • Cutadapt - A tails and other types of unwanted sequence from your high-throughput sequencing reads.
      • bbduk - quality-related trimming, filtering, and masking operations into a single high-performance tool.
      • trimgalore - digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.
      • trimmomatic
      • Sortmerna

    • read merger

    • quality analysis checking

    • demultiplexing

      • fastq-multx - end sequences, and also to allow the "guessing" of barcode sets based on master lists of barcoding protocols (fluidigm, truseq, etc.)
      • NextGenSeqUtils

  • Multiviewer

  • Mapping tools

    • aligner

    • splice-aligner

      • Tophat2 - Seq reads.
      • CRAC - Seq mapping software that include the discovery of transcriptomic and genomic variants like splice junction, chimeric junction, SNVs, Indels in a single analysis step using a built-in error detection method enabling high precison and sensitivity.

  • Assembly tools

  • Variant calling & alternative splicing tools

    • variant calling

      • VarScan
      • KisSplice
      • Farline
      • freebayes - nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.

    • Motif discovery

      • MaxENTScan - adjacent as well as adjacent dependencies between positions.

    • Peak calling

      • MACS2 - sequencing experiment.
      • m6a Viewer - platform java application for detecting and visualising peaks in ME-RIP/ m6a-seq data.

  • Counting tools

    • Correction tools

  • Statistical analysis tools

  • Phylogenomics

    • Aligner

    • Model test

      • SMS - based criteria (e.g., AIC).

    • Phylogenetic inference

      • PhyML
      • RAxML - Randomized Axelerated Maximum Likelihood.
      • FastTree - maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.
      • FastME

    • Visualization

    • Tree comparison

      • CompPhy - based collaborative platform for comparing phylogenies
      • Phylo.io

    • Platform

  • Others

    • Exploration tools

      • RNA-Ribo Explorer (RRE) - alone, and graphical software for analysing, viewing and mining both transcriptome (typically RNA-seq) and translatome (typically Ribosome profiling or Ribo-seq) datasets.
      • IGET - scale gene expression and protein behavior dynamics.

    • Network & Interaction visualisation

    • Clustering & homology

      • CD-HIT - HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.
      • HMMER
      • STRUCTURE - locus genotype data to investigate population structure.

    • Annotations tools

      • Trinotate - model organisms.
      • gProfiler
      • TransDecoder - Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.

    • Ontology & Pathway databases

      • KEGG - level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.
      • DAVID
      • PANTHER
      • RNAcentral - coding RNA sequence database

    • Metabarcoding databases

  • Specific workflow

    • Community analysis

      • Mothur - source, expandable software to fill the bioinformatics needs of the microbial ecology community.
      • QIIME2 - generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.

    • Alternative splicing

  • Bioinformatic analysis informations

Programming Languages
C 3 C++ 1
Categories
Others 17 Phylogenomics 16 Quality analysis & trimming tools 14 Statistical analysis tools 11 Bioinformatic analysis informations 11 Variant calling & alternative splicing tools 7 Assembly tools 6 Counting tools 4 Suite tools 4 Mapping tools 4 Awesome existing topics related to bioinformatics 4 Specific workflow 3 Multiviewer 1
Sub Categories
trimming 6 RNA-seq 5 Correction tools 5 read merger 4 Aligner 4 Ontology & Pathway databases 4 Phylogenetic inference 4 Visualization 4 variant calling 4 Alternative-splicing 3 Annotations tools 3 Clustering & homology 3 MASS-SPEC 3 Network & Interaction visualisation 3 Genome & Transcriptome de novo assembly 3 demultiplexing 3 quality analysis checking 2 Metagenomics 2 Community analysis 2 Metagenome & Metatranscriptome assembly 2 Peak calling 2 splice-aligner 2 aligner 2 Metabarcoding databases 2 Exploration tools 2 Tree comparison 2 Alternative splicing 1 Metatranscriptomic 1 Metagenomic 1 Proteomics 1 Motif discovery 1 Ribo-seq 1 Merip-seq 1 RIBO-seq 1 Metabarcoding 1 Model test 1 mi-CLIP 1 Platform 1 Metabarcoding | Community Ecology 1
Keywords
awesome-list 3 awesome 2 recurrent-networks 1 neural-network 1 machine-learning 1 face-images 1 deep-networks 1 deep-learning-tutorial 1 deep-learning 1 bioinformatics 1 workflow 1