Stars
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
Versatile open-source tool for microbiome analysis
Transcript assembly and quantification for RNA-Seq
GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0
Accurate Species Tree EstimatoR: a family of optimation algorithms for species tree inference (including ASTRAL & CASTER)
base-accurate DNA sequence alignments using WFA and mashmap3
Fast alignment and preprocessing of chromatin profiles
Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation
A fast whole-genome aligner based on de Bruijn graphs
Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.
phylogenetics tools for linux (and other mostly posix compliant) computers
Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.
A single fast and exhaustive tool for summary statistics and simultaneous *fa* (fasta, fastq, gfa [.gz]) genome assembly file manipulation.
MECAT: an ultra-fast mapping, error correction and de novo assembly tool for single-molecule sequencing reads
A pipeline used to identify different modes of duplicated gene pairs
Scallop is a reference-based transcriptome assembler for RNA-seq
The LACHESIS software, as described in Nature Biotechnology (http://dx.doi.org/10.1038/nbt.2727)
A genome assembler that reduces the computational time of human genome assembly from 400,000 CPU hours to 2,000 CPU hours, utilizing long erroneous 3GS sequencing reads and short accurate NGS seque…
Find and visualize rearrangements in DNA sequences
FFT cross-correlation based synteny aligner, (re)designed to make full use of parallel computing
Splice junction analysis and filtering from BAM files