SaiReddy-A

oneliners

Useful bash one-liners for bioinformatics.

gos

A declarative interactive genomics visualization library for Python.

jcvi

Python library to facilitate genome assembly, annotation, and comparative genomics

learngenomics.dev

A guided, intuitive introduction to genomics for software engineers. Curated by the community.

telomeric-identifier

Identify and find telomeres, or telomeric repeats in a genome.

FindTelomeres

A python script for finding telomeric repeats (TTAGGG/CCCTAA) in FASTA files

ALLHiC

ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data

NuclearPhaser

Phasing of dikaryotic fungal genome assemblies

phased-assembly-check

deepconsensus

DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.

vgp-assembly

VGP repository for the genome assembly working group

SALSA

SALSA: A tool to scaffold long read assemblies with Hi-C data

pbbioconda

PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.

fastp

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

3d-dna

3D de novo assembly (3D DNA) pipeline

ALLHiC

ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data

Juicebox

Visualization and analysis software for Hi-C data -

NextPolish

Fast and accurately polish the genome generated by long reads.

Awesome-Bioinformatics

A curated list of awesome Bioinformatics libraries and software.

phandango

an interactive viewer for populations of bacterial genomes linked by a phylogeny

awesome-genome-visualization

A list of interesting genome browser or genome-browser-like implementations

LongStitch

Correct and scaffold assemblies using long reads

AnchorWave

Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation

AHRD

High throughput protein function annotation with Human Readable Description (HRDs) and Gene Ontology (GO) Terms.

GFF3toolkit

Python programs for processing GFF3 files

nanopack

An overview of all nanopack tools

nanostat

Create statistic summary of an Oxford Nanopore read dataset

Porechop

adapter trimmer for Oxford Nanopore reads

bcbb

Incubator for useful bioinformatics code, primarily in Python and R

dotPlotly

Generate an interactive dot plot from mummer or minimap alignments