Assembly tools

Correction tools

• rnaQUAST

Genome & Transcriptome de novo assembly

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

Metagenome & Metatranscriptome assembly

• MetaSPADES
• Megahit - fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
• MetaVelvetSL
• Minia for metagenome - Minia-Pipeline is a de novo assembly pipeline for Illumina data. It can assemble genomes and metagenomes.

Viewers

• Bandage
• IGV

Awesome existing topics related to bioinformatics

• awesome-bioinformatics
• awesome-deep-learning
• awesome-alternative-splicing
• awesome-pipeline

Bioinformatic analysis informations

Alternative-splicing

• Alternative-splicing

MASS-SPEC

• Mass spectrometry in general
• Mass-spec for DNA
• Mass-spec for RNA

Merip-seq

• Merip-seq

Metabarcoding

• Barcoding

Metagenomic

• Metagenomics

Metatranscriptomic

• Metatranscriptomics

mi-CLIP

• Illumina mi-CLIP-m6a

Proteomics

• Proteomics

Ribo-seq

• Ribosome profiling

Counting tools

Correction tools

• FeatureCounts
• Kallisto - cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.
• HTSeqCount - throughput sequencing data with Python
• StringTie - Seq
• RSEM - Seq data.

Mapping tools

aligner

• DIAMOND
• BWA
• PANDASEQ
• MPscan
• Bowtie2 - efficient tool for aligning sequencing reads to long reference sequences.

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.
• STAR

Multiviewer

demultiplexing

• MultiQC

Others

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.

Clustering & homology

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

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.

Metabarcoding databases

• Silva
• FunGuild
• ITS2

Network & Interaction visualisation

• Gephi
• Cytoscape
• String - Protein Interaction Networks Functional Enrichment Analysis

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

Phylogenomics

Aligner

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

Model test

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

Phylogenetic inference

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

Platform

• CIPRES

Tree comparison

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

Visualization

• iTOL
• Krona - layered pie charts.
• Aquapony
• ETE

Quality analysis & trimming tools

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
• UMI-tools - Seq cell barcodes.

quality analysis checking

• FastQC
• FastQ Screen

read merger

• PEAR - efficient and highly accurate pair-end read merger.
• Fastq-join - end reads on the overlapping ends.
• Seq-prep
• FLASH

trimming

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

Specific workflow

Alternative splicing

• KisSplice

Community analysis

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

Statistical analysis tools

Alternative-splicing

• DEX-seq - Seq.
• KissDE - Specific Variants in RNA-Seq Data.

Metabarcoding | Community Ecology

• vegan

Metagenomics

• Metagenassist
• MG-RAST
• MEGAN - MEGAN6 is a comprehensive toolbox for interactively analyzing microbiome data.

RIBO-seq

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

RNA-seq

• DESeq2
• EdgeR
• NBAMSeq
• Sleuth - Seq experiments for which transcript abundances have been quantified with kallisto.
• NOISeq - seq data

Suite tools

• GATK
• 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

Variant calling & alternative splicing tools

Correction tools

• Portcullis - aligned RNA-seq data.

Learning tools

• DeepVariant - generation DNA sequencing data.
• LaBrachoR
• SpliceAI - based tool to identify splice variants
• SpliceAI-wrapper

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.

variant calling

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