| R |
The R Project for Statistical Computing |
| BioPerl |
The Bioperl Project is an international association of users & developers of open source Perl tools for bioinformatics, genomics and life science |
| Biopython |
The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology |
| NCBI BLAST+ |
Basic Local Alignment Search Tool |
| DIAMOND |
Fast and sensitive protein alignment using DIAMOND |
| HMMER |
Accelerated Profile HMM Searches |
| CD-HIT |
CD-HIT: a fast program for clustering and comparing large sets of protein or nucleotide sequences |
| VSEARCH |
VSEARCH: a versatile open source tool for metagenomics |
| MUSCLE |
MUSCLE: multiple sequence alignment with high accuracy and high throughput |
| MAFFT |
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform |
| JAligner |
Open-source Java implementation of the Smith-Waterman algorithms for biological pairwise sequence alignment |
| BWA |
Fast and accurate short read alignment with Burrows–Wheeler transform |
| HISAT2 |
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype |
| Bowtie2 |
Fast gapped-read alignment with Bowtie 2 |
| STAR |
STAR: ultrafast universal RNA-seq aligner |
| Salmon |
Alignment and mapping methodology influence transcript abundance estimation |
| kallisto |
Near-optimal probabilistic RNA-seq quantification |
| BBMap |
BBMerge – Accurate paired shotgun read merging via overlap |
| FASTX |
Collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing |
| Trimmomatic |
Trimmomatic: a flexible trimmer for Illumina sequence data |
| SeqKit |
SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation |
| seqtk |
Toolkit for processing sequences in FASTA/Q formats |
| fastp |
fastp: an ultra-fast all-in-one FASTQ preprocessor |
| HTStream |
A toolset for high throughput sequence analysis using a streaming approach facilitated by Linux pipes |
| fqtrim |
trimming & filtering of next-gen reads |
| TreeTime |
TreeTime: Maximum-likelihood phylodynamic analysis |
| FastTree |
FastTree 2–approximately maximum-likelihood trees for large alignments |
| RAxML |
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies |
| RAxML-NG |
RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference |
| PhyML |
Estimating maximum likelihood phylogenies with PhyML |
| Pplacer |
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree |
| SAMtools |
The Sequence Alignment/Map format and SAMtools |
| BCFtools |
https://www.ncbi.nlm.nih.gov/pubmed/28205675 |
| Bamtools |
BamTools provides both a programmer’s API and an end-user’s toolkit for handling BAM files |
| VCFtools |
The Variant Call Format and VCFtools |
| BEDTools |
BEDTools: a flexible suite of utilities for comparing genomic features |
| deepTools |
deepTools2: a next generation web server for deep-sequencing data analysis |
| BEDOPS |
BEDOPS: high-performance genomic feature operations |
| Sambamba |
Sambamba: fast processing of NGS alignment formats |
| SPAdes |
SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing |
| ABySS |
ABySS: a parallel assembler for short read sequence data |
| Velvet |
Velvet: algorithms for de novo short read assembly using de Bruijn graphs |
| MEGAHIT |
MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph |
| MetaVelvet |
MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads |
| Prodigal |
Prodigal: prokaryotic gene recognition and translation initiation site identification |
| Infernal |
inference of RNA alignments |
| antiSMASH |
antiSMASH: Rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters |
| DeepBGC |
A deep learning genome-mining strategy for biosynthetic gene cluster prediction |
| GECCO |
Accurate de novo identification of biosynthetic gene clusters with GECCO |
| Miniconda |
Package, dependency and environment management for any language |
| CD-HIT |
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences |
| Nextflow |
Nextflow enables reproducible computational workflows |
| GATK |
The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data |
| Centrifuge |
Centrifuge: rapid and sensitive classification of metagenomic sequences |
| Pavian |
Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification |
| Kraken2 |
Metagenome analysis using the Kraken software suite |
| Bracken |
Bracken: estimating species abundance in metagenomics data |
| MetaPhlAn |
Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4 |
| HUMAnN |
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 |
| mothur |
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities |
| UCHIME |
UCHIME improves sensitivity and speed of chimera detection |
