Trinity RNA-Seq de novo transcriptome assembly

TransDecoder source

MACS -- Model-based Analysis of ChIP-Seq

GeneMark-ETP: gene finding in eukaryotic genomes supported by transcriptome sequencing and protein homology

PASA software

source code for EVM

Valid and Powerful Machine-Learning-Assisted Genetic Association Studies

Eukaryotic Genome Annotation Pipeline-External caller scripts and documentation

Using Deep Learning to predict gene annotations

Visualization and analysis software for Hi-C data -

Automatically exported from code.google.com/p/cdhit

TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes

Make colorful identity heatmaps of genomic sequence

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

A Tool for integrated Quality Control and Preprocessing on FASTQ or BAM/CRAM files

Mummer alignment tool

3D de novo assembly (3D DNA) pipeline

HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data

PacBio BAM toolkit

Automatically exported from code.google.com/p/figtree

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

A novel genome assembly pipeline based on deep learning

A new simple and efficient software to PCA and Cluster For popolation VCF File

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

The next version of bwa-mem

A fast and sensitive gapped read aligner

R toolkit for single cell genomics