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awesome-bioinfo-tools

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

Last synced: about 18 hours ago
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  • Variant calling & alternative splicing tools

    • Motif discovery

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

    • Learning tools

    • variant calling

      • VarScan
      • KisSplice
      • 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.
      • Farline
      • SplAdder - Seq alignment data.
      • Whippet

    • Correction tools

    • Peak calling

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

  • Specific workflow

    • Community analysis

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

    • Alternative splicing

  • Quality analysis & trimming tools

  • Phylogenomics

    • Phylogenetic inference

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

    • Visualization

    • Tree comparison

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

    • Platform

    • Aligner

      • RAPPAS - free phylogenetic identification of metagenomic sequences.
      • RAPPAS - free phylogenetic identification of metagenomic sequences.
      • Clustalw
      • MAFFT
      • MEGA

    • Model test

      • SMS - based criteria (e.g., AIC).
      • ModelTest-NG - NG is a tool for selecting the best-fit model of evolution for DNA and protein alignments.
      • jModelTest2 - fit models of nucleotide substitution.
      • SMS - based criteria (e.g., AIC).

  • Others

    • Exploration tools

      • IGET - scale gene expression and protein behavior dynamics.
      • 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.
      • 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.

    • Network & Interaction visualisation

    • Clustering & homology

      • HMMER
      • 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.

    • Ontology & Pathway databases

      • Gene Ontology
      • DAVID
      • PANTHER
      • 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
      • RNAcentral - coding RNA sequence database

    • Metabarcoding databases

    • 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.

  • Mapping tools

    • aligner

    • splice-aligner

      • Tophat2 - Seq reads.
      • STAR
      • 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.

  • Suite tools

    • BBtools
    • GATK
    • BBtools
    • BBtools
    • 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.

  • Multiviewer

  • Assembly tools

    • Genome & Transcriptome de novo assembly

      • Velvet
      • SPAdes
      • Minia - read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.
      • Trinity - Seq data.

    • Metagenome & Metatranscriptome assembly

    • Correction tools

    • Viewers

  • Counting tools

    • Correction tools

  • Statistical analysis tools

    • RNA-seq

    • RIBO-seq

      • Anota2Seq - wide analysis of translational efficiency using anota2seq.
      • Xtail - wide assessment of differential translations with ribosome profiling data.

    • Metabarcoding | Community Ecology

    • Alternative-splicing

    • Metagenomics

  • Bioinformatic analysis informations

Programming Languages
C++ 7 C 5 Python 4 Java 1 Jupyter Notebook 1 Perl 1 R 1
Categories
Phylogenomics 29 Others 22 Quality analysis & trimming tools 17 Variant calling & alternative splicing tools 15 Statistical analysis tools 12 Assembly tools 11 Bioinformatic analysis informations 11 Mapping tools 9 Suite tools 6 Counting tools 5 Specific workflow 4 Awesome existing topics related to bioinformatics 4 Multiviewer 1
Sub Categories
Phylogenetic inference 9 Correction tools 7 trimming 7 aligner 6 Visualization 6 variant calling 6 Ontology & Pathway databases 6 RNA-seq 5 Metagenome & Metatranscriptome assembly 5 Aligner 5 demultiplexing 4 Genome & Transcriptome de novo assembly 4 read merger 4 Model test 4 Learning tools 4 Clustering & homology 4 Annotations tools 3 Alternative-splicing 3 quality analysis checking 3 Community analysis 3 Tree comparison 3 Network & Interaction visualisation 3 MASS-SPEC 3 Exploration tools 3 splice-aligner 3 Metabarcoding databases 3 Platform 2 Peak calling 2 Metagenomics 2 RIBO-seq 2 Motif discovery 2 Proteomics 1 Metagenomic 1 Metatranscriptomic 1 Merip-seq 1 Metabarcoding 1 Alternative splicing 1 mi-CLIP 1 Viewers 1 Ribo-seq 1 Metabarcoding | Community Ecology 1
Keywords
bioinformatics 6 genomics 3 awesome-list 3 sequence-alignment 2 metagenomics 2 machine-learning 2 deep-learning 2 awesome 2 face-images 1 neural-network 1 recurrent-networks 1 deep-networks 1 workflow 1 deep-neural-network 1 deepvariant 1 deep-learning-tutorial 1 dna 1 genome 1 ngs 1 science 1 research-tool 1 phylogenetics 1 markov-chain-monte-carlo 1 bayesian-inference 1 search 1 microbiome 1 metabarcoding 1 fastq 1 fasta 1 clustering 1 chimera 1 amplicon 1 succinct 1 genome-assembly 1 data-structures 1 fm-index 1 tensorflow 1 sequencing 1