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3d-dna

3D de novo assembly (3D DNA) pipeline

alphafold

Install alphafold on the local machine, get out of docker.

bamkit

Tools for common BAM file manipulations

bsalign

Banded Striped DNA Sequence Alignment

bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

caas_practicalbioinformatics_2020aut

cnvnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads

dotplotly

Generate an interactive dot plot from mummer or minimap alignments

edlib

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.

edta

Extensive de-novo TE Annotator

freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

genomeworks

SDK for GPU accelerated genome assembly and analysis

git-bash-here

gwa_tutorial

A comprehensive tutorial about GWAS and PRS

gwastutorial

Genome-wide association studies tutorial 🧬

haphic

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

helixer

Using Deep Learning to predict gene annotations

hypo-assembler

i-at-lsphere

Collection of genome-scale metabolic models, genomes, and scripts for At-LSPHERE bacterial culture collection

jasmine

Jasmine: SV Merging Across Samples

ltr_retriever

LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.

lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery

maize_genomic_ecosystem

miniforge

A conda-forge distribution.

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

newick_utils

shell tools for processing phylogenetic trees

orthofinder

Phylogenetic orthology inference for comparative genomics

owltools

OWLTools

pandagma

Generate pan-gene sets, given a collection of genome assemblies and corresponding gene models.

phylomint

Pathway-based and phylogenetically adjusted quantification of competition and cooperation between microbial species