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https://github.com/RipollJ/awesome-bioinfo-tools

A curated list of awesome Bioinformatics tools.
https://github.com/RipollJ/awesome-bioinfo-tools
List: awesome-bioinfo-tools
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A curated list of awesome Bioinformatics tools.
Host: GitHub
URL: https://github.com/RipollJ/awesome-bioinfo-tools
Owner: RipollJ
Created: 2020-05-06T20:06:22.000Z (over 4 years ago)
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Last Pushed: 2020-05-06T20:06:43.000Z (over 4 years ago)
Last Synced: 2024-12-02T06:02:30.394Z (19 days ago)
Topics: awesome-list, bioinformatics, bioinformatics-analysis, bioinformatics-tool
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- Readme: README.md
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README

        # Awesome Bioinfo-tools

A curated list of awesome Bioinformatics tools.

----------------------------------------------------------------------------

Table of contents

- [Awesome Bioinfo-tools](#awesome-bioinfo-tools)

  * [Awesome existing topics related to bioinformatics](#awesome-existing-topics-related-to-bioinformatics)

  * [Suite tools](#suite-tools)

  * [Quality analysis & trimming tools](#quality-analysis---trimming-tools)

    + [quality analysis checking](#quality-analysis-checking)

    + [trimming](#trimming)

    + [read merger](#read-merger)

    + [demultiplexing](#demultiplexing)

  * [Multiviewer](#multiviewer)

  * [Mapping tools](#mapping-tools)

    + [aligner](#aligner)

    + [splice-aligner](#splice-aligner)

  * [Assembly tools](#assembly-tools)

    + [Genome & Transcriptome de novo assembly](#genome---transcriptome-de-novo-assembly)

    + [Metagenome & Metatranscriptome assembly](#metagenome---metatranscriptome-assembly)

    + [Viewers](#viewers)

    + [Correction tools](#correction-tools)

  * [Variant calling & alternative splicing tools](#variant-calling---alternative-splicing-tools)

    + [variant calling](#variant-calling)

    + [Motif discovery](#motif-discovery)

    + [Peak calling](#peak-calling)

    + [Learning tools](#learning-tools)

    + [Correction tools](#correction-tools-1)

  * [Counting tools](#counting-tools)

  * [Statistical analysis tools](#statistical-analysis-tools)

    + [RNA-seq](#rna-seq)

    + [Metagenomics](#metagenomics)

    + [Metabarcoding | Community Ecology](#metabarcoding---community-ecology)

    + [Alternative-splicing](#alternative-splicing)

    + [RIBO-seq](#ribo-seq)

  * [Phylogenomics](#phylogenomics)

    + [Aligner](#aligner)

    + [Phylogenetic inference](#phylogenetic-inference)

    + [Model test](#model-test)

    + [Visualization](#visualization)

    + [Tree comparison](#tree-comparison)

    + [Platform](#platform)

  * [Others](#others)

    + [Exploration tools](#exploration-tools)

    + [Network & Interaction visualisation](#network---interaction-visualisation)

    + [Clustering & homology](#clustering---homology)

    + [Annotations tools](#annotations-tools)

    + [Ontology & Pathway databases](#ontology---pathway-databases)

    + [Metabarcoding databases](#metabarcoding-databases)

  * [Specific workflow](#specific-workflow)

    + [Alternative splicing](#alternative-splicing)

    + [Community analysis](#community-analysis)

  * [Bioinformatic analysis informations](#bioinformatic-analysis-informations)

    + [Metagenomic](#metagenomic)

    + [Metatranscriptomic](#metatranscriptomic)

    + [Metabarcoding](#metabarcoding)

    + [Alternative-splicing](#alternative-splicing-1)

    + [Ribo-seq](#ribo-seq)

    + [Merip-seq](#merip-seq)

    + [mi-CLIP](#mi-clip)

    + [Proteomics](#proteomics)

    + [MASS-SPEC](#mass-spec)

----------------------------------------------------------------------------

## Awesome existing topics related to bioinformatics

- [awesome-bioinformatics](https://github.com/danielecook/Awesome-Bioinformatics): some informations on Bioinformatics.

- [awesome-alternative-splicing](https://github.com/HussainAther/awesome-alternative-splicing): some programs for alternative splicing analysis.

- [awesome-pipeline](https://github.com/pditommaso/awesome-pipeline): found the best pipeline workflow for your applications.

- [awesome-deep-learning](https://github.com/ChristosChristofidis/awesome-deep-learning): deep learning informations.

[[top↑]](#)

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## Suite tools

- [BBtools](https://jgi.doe.gov/data-and-tools/bbtools/): BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data. 

- [samtools](https://github.com/samtools/samtools): The original samtools package has been split into three separate but tightly coordinated projects:

    - htslib: C-library for handling high-throughput sequencing data

    - samtools: mpileup and other tools for handling SAM, BAM, CRAM

    - bcftools: calling and other tools for handling VCF, BCF

- [GATK](https://gatk.broadinstitute.org/hc/en-us): A genomic analysis toolkit focused on variant discovery.

- [EA-Utils](https://expressionanalysis.github.io/ea-utils/): Command-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.

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## Quality analysis & trimming tools

### quality analysis checking

- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/): A quality control tool for high throughput sequence data.

- [FastQ Screen](http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/_build/html/index.html): FastQ Screen is a simple application which allows you to search a large sequence dataset against a panel of different genomes to determine from where the sequences in your data originate.

### trimming

- [Sickle](https://github.com/najoshi/sickle): A windowed adaptive trimming tool for FASTQ files using quality.

- [Cutadapt](https://cutadapt.readthedocs.io/en/stable/index.html): Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.

- [bbduk](https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbduk-guide/): “Duk” stands for Decontamination Using Kmers. BBDuk was developed to combine most common data-quality-related trimming, filtering, and masking operations into a single high-performance tool. 

- [trimgalore](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/): A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.

- [trimmomatic](http://www.usadellab.org/cms/?page=trimmomatic): A flexible read trimming tool for Illumina NGS data.

- [Sortmerna](https://bioinfo.lifl.fr/RNA/sortmerna/): Fast filtering, mapping and OTU picking.

### read merger

- [PEAR](https://cme.h-its.org/exelixis/web/software/pear/doc.html): PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. 

- [Fastq-join](https://github.com/ExpressionAnalysis/ea-utils/blob/wiki/FastqJoin.md): Joins two paired-end reads on the overlapping ends.

- [Seq-prep](https://github.com/jstjohn/SeqPrep): SeqPrep is a program to merge paired end Illumina reads that are overlapping into a single longer read.

- [FLASH](http://ccb.jhu.edu/software/FLASH/): Fast Length Adjustment of SHort reads

### demultiplexing

- [fastq-multx](https://github.com/ExpressionAnalysis/ea-utils/blob/wiki/FastqMultx.md): The goal of this program is to make it easier to demultiplex possibly paired-end sequences, and also to allow the "guessing" of barcode sets based on master lists of barcoding protocols (fluidigm, truseq, etc.)

- [UMI-tools](https://github.com/CGATOxford/UMI-tools): This repository contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes.

- [NextGenSeqUtils](https://nextjournal.com/Murrell-Lab/demultiplexing-with-custom-barcoded-primers): Notebook for demultiplexing with custom barcoded primers.

[[top↑]](#)

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## Multiviewer

- [MultiQC](https://multiqc.info/): Aggregate results from bioinformatics analyses across many samples into a single report.

[[top↑]](#)

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## Mapping tools

### aligner

- [BWA](https://github.com/lh3/bwa): BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome. 

- [Bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml): Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.

- [PANDASEQ](https://github.com/neufeld/pandaseq): PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.

- [MPscan](http://www.atgc-montpellier.fr/mpscan/): MPscan: index free mapping of multiple short reads on a genome

- [DIAMOND](http://www.diamondsearch.org/index.php): DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data.

### splice-aligner

- [Tophat2](https://ccb.jhu.edu/software/tophat/index.shtml): TopHat is a fast splice junction mapper for RNA-Seq reads.

- [STAR](https://github.com/alexdobin/STAR): Spliced Transcripts Alignment to a Reference.

- [CRAC](http://crac.gforge.inria.fr/): RNA-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.

[[top↑]](#)

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## Assembly tools

### Genome & Transcriptome de novo assembly

- [Velvet](https://www.ebi.ac.uk/~zerbino/velvet/): Sequence assembler for very short reads

- [SPAdes](http://cab.spbu.ru/files/release3.12.0/manual.html): SPAdes – St. Petersburg genome assembler – is an assembly toolkit containing various assembly pipelines.

- [Minia](https://github.com/GATB/minia): Minia is a short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.

- [Trinity](https://github.com/trinityrnaseq/trinityrnaseq/wiki): Trinity assembles transcript sequences from Illumina RNA-Seq data.

### Metagenome & Metatranscriptome assembly

- [Megahit](https://github.com/voutcn/megahit): An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

- [MetaVelvetSL](http://metavelvet.dna.bio.keio.ac.jp/MSL.html): An extension of Velvet assembler to de novo metagenomic assembly

- [MetaSPADES](https://kbase.us/applist/apps/kb_SPAdes/run_metaSPAdes/release?gclid=CjwKCAjwwMn1BRAUEiwAZ_jnEkxHhKIJi9wEvB5wcMs818fq2fFTmdO_-2Dz3EP015_QPbgdBO73tRoCdxoQAvD_BwE): Assemble metagenomic reads using the SPAdes assembler.

- [Minia for metagenome](https://github.com/GATB/gatb-minia-pipeline): GATB-Minia-Pipeline is a de novo assembly pipeline for Illumina data. It can assemble genomes and metagenomes.

### Viewers

- [Bandage](https://rrwick.github.io/Bandage/): Bandage is a program for visualising de novo assembly graphs.

- [IGV](http://software.broadinstitute.org/software/igv/): visualization tool for interactive exploration of large, integrated genomic datasets.

### Correction tools

- [rnaQUAST](http://cab.spbu.ru/software/rnaquast/): rnaQUAST is a software designed for quality evaluation and assessment of de novo transcriptome assemblies. 

[[top↑]](#)

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## Variant calling & alternative splicing tools

### variant calling

- [VarScan](http://varscan.sourceforge.net/): variant detection in massively parallel sequencing data.

- [KisSplice](http://kissplice.prabi.fr/): A local transcriptome assembler for SNPs, indels and AS events

- [Farline](http://fasterdb.ens-lyon.fr/tools.php): FaRLine is a pipeline to analyse the alternative splicing.

- [SplAdder](https://github.com/ratschlab/spladder): SplAdder, short for Splicing Adder, a toolbox for alternative splicing analysis based on RNA-Seq alignment data.

- [Whippet](https://github.com/timbitz/Whippet.jl): Efficient and Accurate Quantitative Profiling of Alternative Splicing Patterns of Any Complexity on a Laptop.

- [freebayes](https://github.com/ekg/freebayes/blob/master/README.md): freebayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-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](http://hollywood.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq.html): MaxEntScan is based on the approach for modeling the sequences of short sequence motifs such as those involved in RNA splicing which simultaneously accounts for non-adjacent as well as adjacent dependencies between positions.

### Peak calling

- [MACS2](https://hbctraining.github.io/Intro-to-ChIPseq/lessons/05_peak_calling_macs.html): computational method used to identify areas in the genome that have been enriched with aligned reads as a consequence of performing a ChIP-sequencing experiment.

- [m6a Viewer](http://dna2.leeds.ac.uk/m6a/): m6a Viewer is a cross-platform java application for detecting and visualising peaks in ME-RIP/ m6a-seq data. 

### Learning tools

- [DeepVariant](https://github.com/google/deepvariant): DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. 

- [LaBrachoR](https://github.com/jpaggi/labranchor): LaBranchoR uses a LSTM network built with keras to predict the position of RNA splicing branchpoints relative to a three prime splice site.

- [SpliceAI](https://github.com/Illumina/SpliceAI): A deep learning-based tool to identify splice variants

- [SpliceAI-wrapper](https://github.com/bihealth/spliceai-wrapper): SpliceAI Wrapper, is an attempt to use caching for reducing the number of required predictions. Please note that the authors of SpliceAI Wrapper are unrelated to the authors of SpliceAI.

### Correction tools

- [Portcullis](https://github.com/TGAC/portcullis): Portcullis stands for PORTable CULLing of Invalid Splice junctions from pre-aligned RNA-seq data. 

[[top↑]](#)

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## Counting tools

- [FeatureCounts](http://bioinf.wehi.edu.au/featureCounts/): counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations.

- [Kallisto](https://pachterlab.github.io/kallisto/about): kallisto is a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. 

- [HTSeqCount](https://htseq.readthedocs.io/en/master/): Analysing high-throughput sequencing data with Python

- [StringTie](https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual#top): Transcript assembly and quantification for RNA-Seq

- [RSEM](https://github.com/deweylab/RSEM): RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. 

[[top↑]](#)

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## Statistical analysis tools

### RNA-seq

- [DESeq2](https://bioconductor.org/packages/release/bioc/html/DESeq2.html): Differential gene expression analysis based on the negative binomial distribution.

- [EdgeR](https://bioconductor.org/packages/release/bioc/html/edgeR.html): Empirical Analysis of Digital Gene Expression Data in R.

- [NBAMSeq](https://bioconductor.org/packages/release/bioc/html/NBAMSeq.html): NBAMSeq is a Bioconductor package for differential expression analysis based on negative binomial additive model.

- [NOISeq](http://bioconductor.org/packages/release/bioc/html/NOISeq.html): Exploratory analysis and differential expression for RNA-seq data

- [Sleuth](https://pachterlab.github.io/sleuth/about): sleuth is a program for analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto. 

### Metagenomics

- [Metagenassist](http://www.metagenassist.ca/METAGENassist/faces/Home.jsp): A comprehensive web server for comparative metagenomics

- [MG-RAST](https://www.mg-rast.org/): A Metagenomics Service for Analysis of Microbial Community Structure and Function.

- [MEGAN](https://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/algorithms-in-bioinformatics/software/megan6/): Metagenome Analyzer - MEGAN6 is a comprehensive toolbox for interactively analyzing microbiome data. 

### Metabarcoding | Community Ecology

- [vegan](https://www.rdocumentation.org/packages/vegan/versions/2.4-2): Ordination methods, diversity analysis and other functions for community and vegetation ecologists.

### Alternative-splicing

- [DEX-seq](https://bioconductor.org/packages/release/bioc/html/DEXSeq.html): Inference of differential exon usage in RNA-Seq.

- [KissDE](https://bioconductor.org/packages/release/bioc/html/kissDE.html): Retrieves Condition-Specific Variants in RNA-Seq Data.

### RIBO-seq

- [Xtail](https://github.com/xryanglab/xtail): Genome-wide assessment of differential translations with ribosome profiling data.

- [Anota2Seq](https://bioconductor.org/packages/release/bioc/html/anota2seq.html): Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq.

[[top↑]](#)

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## Phylogenomics

### Aligner

- [RAPPAS](http://www.atgc-montpellier.fr/RAPPAS/): RAPPAS: Rapid alignment-free phylogenetic identification of metagenomic sequences.

- [Clustalw](https://www.genome.jp/tools-bin/clustalw): Multiple Sequence Alignment.

- [MEGA](https://www.megasoftware.net/): Molecular Evolutionary Genetics Analysis.

- [MAFFT](https://mafft.cbrc.jp/alignment/software/): Multiple alignment program for amino acid or nucleotide sequences.

- [MUSCLE](https://www.ebi.ac.uk/Tools/msa/muscle/): MUSCLE stands for MUltiple Sequence Comparison by Log- Expectation. 

### Phylogenetic inference

- [PhyML](http://www.atgc-montpellier.fr/phyml/): PhyML is a software package that uses modern statistical approaches to analyse alignments of nucleotide or amino acid sequences in a phylogenetic framework. 

- [RAxML](https://cme.h-its.org/exelixis/web/software/raxml/): RAxML - Randomized Axelerated Maximum Likelihood.

- [FastTree](http://www.microbesonline.org/fasttree/): FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.

- [FastME](http://www.atgc-montpellier.fr/fastme/): FastME provides distance algorithms to infer phylogenies.

- [MrBayes](http://nbisweden.github.io/MrBayes/): MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models.

### Model test

- [jModelTest2](https://github.com/ddarriba/jmodeltest2): jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution.

- [ModelTest-NG](https://github.com/ddarriba/modeltest): ModelTest-NG is a tool for selecting the best-fit model of evolution for DNA and protein alignments.

- [SMS](http://www.atgc-montpellier.fr/sms/): Smart Model Selection using likelihood-based criteria (e.g., AIC).

### Visualization

- [Aquapony](http://www.atgc-montpellier.fr/aquapony/): Visualization and interpretation of phylogeographic information on phylogenetic trees

- [iTOL](https://itol.embl.de/): Interactive Tree Of Life is an online tool for the display, annotation and management of phylogenetic trees.

- [ETE](http://etetoolkit.org/): A Python framework for the analysis and visualization of trees.

- [Krona](https://github.com/marbl/Krona/wiki): Krona allows hierarchical data to be explored with zooming, multi-layered pie charts.

### Tree comparison

- [CompPhy](http://www.atgc-montpellier.fr/compphy/): A web-based collaborative platform for comparing phylogenies

- [Phylo.io](https://phylo.io/): A web app and library for visualising and comparing phylogenetic trees.

### Platform

- [CIPRES](http://www.phylo.org/index.php): The CIPRES Science Gateway V. 3.3 is a public resource for inference of large phylogenetic trees. 

[[top↑]](#)

------------------------------------------------------------------------

## Others

### Exploration tools

- [RNA-Ribo Explorer (RRE)](http://www.atgc-montpellier.fr/rre/): RRE is an interactive, stand-alone, and graphical software for analysing, viewing and mining both transcriptome (typically RNA-seq) and translatome (typically Ribosome profiling or Ribo-seq) datasets.

- [IGET](https://iget.c2b2.columbia.edu/): The Integrated Genomics Exploration Tools (IGET) website provides online access to a suite of tools for exploring biological pathways and DNA/RNA/protein regulatory elements associated with large-scale gene expression and protein behavior dynamics.

### Network & Interaction visualisation

- [Gephi](https://gephi.org/): visualization and exploration software for all kinds of graphs and networks. 

- [Cytoscape](https://cytoscape.org/): visualization of complex networks and integrating these with any type of attribute data. 

- [String](https://string-db.org/): Protein-Protein Interaction Networks Functional Enrichment Analysis

### Clustering & homology

- [CD-HIT](http://weizhongli-lab.org/cd-hit/): CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.

- [HMMER](http://hmmer.org/): HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. 

- [STRUCTURE](https://web.stanford.edu/group/pritchardlab/structure.html): The program structure is a free software package for using multi-locus genotype data to investigate population structure.

### Annotations tools

- [Trinotate](https://github.com/Trinotate/Trinotate.github.io/wiki): Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. 

- [gProfiler](https://biit.cs.ut.ee/gprofiler/gost): g:Profiler is a public web server for characterising and manipulating gene lists. 

- [TransDecoder](https://github.com/TransDecoder/TransDecoder/wiki): TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.

### Ontology & Pathway databases

- [Gene Ontology](http://geneontology.org/): The Gene Ontology (GO) knowledgebase is the world’s largest source of information on the functions of genes.

- [KEGG](https://www.genome.jp/kegg/): KEGG is a database resource for understanding high-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](https://david.ncifcrf.gov/): Database for Annotation, Visualization and Integrated Discovery (DAVID).

- [PANTHER](http://www.pantherdb.org/): Protein ANalysis THrough Evolutionary Relationships.

- [RNAcentral](https://rnacentral.org/): The non-coding RNA sequence database

### Metabarcoding databases

- [Silva](https://www.arb-silva.de/): SILVA provides comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya).

- [ITS2](http://its2.bioapps.biozentrum.uni-wuerzburg.de/): Internal transcribed spacer 2 (ITS2) ribosomal RNA Database 

- [FunGuild](https://github.com/UMNFuN/FUNGuild): Over 13,000 fungal taxa now included in the database & functional annotation tools.

[[top↑]](#)

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## Specific workflow

### Alternative splicing

- [KisSplice](http://kissplice.prabi.fr/training/): Training alternative splicing analysis with KisSplice & suite tools.

### Community analysis

- [QIIME2](https://qiime2.org/): QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.

- [Mothur](https://mothur.org/): This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.

- [Vsearch](https://github.com/torognes/vsearch): Open source tool for metagenomics.

[[top↑]](#)

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## Bioinformatic analysis informations

### Metagenomic

- [Metagenomics](https://en.wikipedia.org/wiki/Metagenomics)

### Metatranscriptomic

- [Metatranscriptomics](https://en.wikipedia.org/wiki/Metatranscriptomics)

### Metabarcoding

- [Barcoding](https://fr.wikipedia.org/wiki/Barcoding_mol%C3%A9culaire)

### Alternative-splicing

- [Alternative-splicing](https://en.wikipedia.org/wiki/Alternative_splicing)

### Ribo-seq

- [Ribosome profiling](https://en.wikipedia.org/wiki/Ribosome_profiling)

### Merip-seq

- [Merip-seq](https://en.wikipedia.org/wiki/MeRIPseq)

### mi-CLIP

- [Illumina mi-CLIP-m6a](https://emea.illumina.com/science/sequencing-method-explorer/kits-and-arrays/miclip-m6a.html)

### Proteomics

- [Proteomics](https://en.wikipedia.org/wiki/Proteomics)

### MASS-SPEC

- [Mass spectrometry in general](https://en.wikipedia.org/wiki/Mass_spectrometry)

- [Mass-spec for DNA](https://www.ncbi.nlm.nih.gov/pubmed/15829234)

- [Mass-spec for RNA](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2442014/)

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