Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.

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python HTML shell docker aws bioinformatics snakemake aws-lambda pipelines conda cwl aws-step-function wdl-workflow cwl-workflow snakemake-workflow

NeuroSEED

Implementation of Neural Distance Embeddings for Biological Sequences (NeuroSEED) in PyTorch (NeurIPS 2021)

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python Jupyter Notebook cython machine-learning bioinformatics pytorch biological-sequences hierarchical-clustering multiple-sequence-alignment neurips-2021

hotsub

Command line tool to run batch jobs concurrently with ETL framework on AWS or other cloud computing resources

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go shell Dockerfile TeX Common Workflow Language wdl docker aws workflow bioinformatics workflow-engine gcp docker-machine batch-job cwl etl-framework wdl-workflow cwl-workflow

slamdunk

Streamlining SLAM-seq analysis with ultra-high sensitivity

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python r shell Dockerfile bioinformatics rna-seq docker-image pypi computational-biology quant-seq slamseq transcription

Binning refiner

Improving genome bins through the combination of different binning programs

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python r bioinformatics metagenomics refinement binning binning-refiner

admixr

An R package for reproducible and automated ADMIXTOOLS analyses

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r Makefile bioinformatics popgen rstats population-genetics

codon-usage-tables

📊 Codon usage tables in code-friendly format + Python bindings

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python bioinformatics synbio codon-optimization codon-usage

paccmann datasets

pytoda - PaccMann PyTorch Dataset Classes. Read the docs: https://paccmann.github.io/paccmann_datasets/

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python bioinformatics deep-learning pytorch rdkit chemoinformatics smiles

rkmh

Classify sequencing reads using MinHash.

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C++HTML python bioinformatics nanopore openmp mutations minhash kmer

sirius

SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)

CeleScope

Single Cell Analysis Pipelines

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python HTML CSS perl r wdl bioinformatics single-cell-analysis

GRAFIMO

GRAph-based Finding of Individual Motif Occurrences

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python cython shell Dockerfile bioinformatics motif-scanning genome-variation-graphs genomic-variants haplotype-aware

awesome-phages

A curated list of phage related software and computational resources for phage scientists, bioinformaticians and enthusiasts.

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bioinformatics bacteria phages bacteriophages

dysgu

dysgu-SV is a collection of tools for calling structural variants using short or long reads

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c cython C++python Jupyter Notebook shell Dockerfile bioinformatics genomics long-read variant-calling structural-variation paired-end

protwis

Protwis is the backbone of the GPCRdb. The GPCRdb contains reference data, interactive visualisation and experiment design tools for G protein-coupled receptors (GPCRs).

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python javascript HTML CSS bioinformatics cheminformatics open-science drug-discovery drug-design hacktoberfest pharmacogenomics chemogenomics gpcr

BridgeDb

The BridgeDb Library source code

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java perl shell CSS HTML r bioinformatics database uri mysql-backend hacktoberfest bridgedb identifier-mapping

sample-sheet

A permissively licensed library designed to replace Illumina's Experiment Manager

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python bioinformatics illumina demultiplexing experiment-manager samplesheet

gnparser

GNparser normalises scientific names and extracts their semantic elements.

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go CSS HTML Makefile Ragel Nix Dockerfile parser bioinformatics nomenclature biodiversity scientific-names

TeamTeri

Genomics using open source tools, running on GCP or AWS

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shell Dockerfile aws bioinformatics gcp gatk variants cancer-genomics genome-sequencing genome-analysis variant-calls genomics-analysis

unimap

A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment

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c Roff Makefile bioinformatics genomics sequence-alignment

PrimerMiner

R mased batch sequence downloader, with primer development and in silico evaluation capabilities

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r bioinformatics ncbi metabarcoding batch-download primer-design boldsystems database-mining

wgs2ncbi

Toolkit for preparing genomes for submission to NCBI

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perl scala TeX shell bioinformatics genomics dataset genome-annotation

PHAT

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

CANDO

Computational Analysis of Novel Drug Opportunities

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python Jupyter Notebook machine-learning bioinformatics shotgun biomedical-informatics drug-discovery drug-repurposing docking drug-design multitarget

Scaff10X

Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads

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c bioinformatics genomics genome scaffolding breaking 10xgenomics

ensembl-compara

The Ensembl Compara Perl API and SQL schema

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perl python java shell r XS mysql api bioinformatics database ensembl comparative-genomics

faster lmm d

A faster lmm for GWAS. Supports GPU backend.

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d shell Makefile bioinformatics gwas genomics gpu opencl arrayfire gwas-tools

jgi-query

A simple command-line tool to download data from Joint Genome Institute databases

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python cli bioinformatics genomics genomes

paladin

Protein Alignment and Detection Interface

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c python C++bioinformatics uniprot unh paladin protein-alignment nucleotide-alignment

gcMapExplorer

Genome Contact Map Explorer - gcMapExplorer. Visit:

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python c bioinformatics hi-c genomic-data-analysis

klib.nim

Experimental getopt, gzip reader, FASTA/Q parser and interval queries in nim-lang

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nim bioinformatics

InSilicoSeq

🚀 A sequencing simulator

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python Dockerfile bioinformatics simulation sequencing metagenomics illumina-sequencing

crimson

Bioinformatics tool outputs converter to JSON or YAML

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python Makefile Dockerfile yaml converter json bioinformatics

open-cravat

A modular annotation tool for genomic variants

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javascript python CSS HTML Jupyter Notebook bioinformatics genomics bioinformatics-pipeline annotation-tool variant-annotations variant-annotation variant-analysis genomic-data-analysis bioinformatics-tool

hts-python

pythonic wrapper for htslib

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python c shell bioinformatics genomics sam bam htslib

ribotricer

A tool for accurately detecting actively translating ORFs from Ribo-seq data

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python shell Makefile bioinformatics translation orfs ribosome-profiling riboseq ribosome translation-regulation

propy3

A Python 3 version of the protein descriptor package propy

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python Makefile bioinformatics protein-sequence dipeptide-composition-descriptors protein-descriptor geary-autocorrelation-descriptors

CellBench

R package for benchmarking single cell analysis methods

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HTML r benchmark bioinformatics

jannovar

Annotation of VCF variants with functional impact and from databases (executable+library)

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java HTML ANTLR python Makefile Batchfile bioinformatics vcf variant-annotation variant-filtration

NGI-RNAseq

Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.

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bioinformatics rna-seq pipeline rnaseq rna-sequencing

cath-tools

Protein structure comparison tools such as SSAP and SNAP

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C++HTML CMake bioinformatics biology pdb structure protein alignment ssap orengo cath superposition ucl cath-resolve-hits

IsoQuant

Reference-based transcript discovery from long RNA read

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python bioinformatics rna-seq nanopore ngs pacbio transcriptomics

poly

A Go package for engineering organisms.

dentist

Close assembly gaps using long-reads at high accuracy.

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d shell python docker bioinformatics snakemake cluster singularity dub pacbio genome-assembly daligner long-reads gap-filling close-assembly-gaps damapper

souporcell

Clustering scRNAseq by genotypes

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python rust Singularity bioinformatics genomics computational-biology scrna-seq scrnaseq scrna-seq-analysis

SeqVec

Modelling the Language of Life - Deep Learning Protein Sequences

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bioinformatics protein-structure protein protein-function

fuc

Frequently used commands in bioinformatics

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python visualization api cli bioinformatics sam vcf fasta gtf bed maf bam fastq cram gff

xpclr

Code to compute the XP-CLR statistic to infer natural selection

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python shell bioinformatics genetics popgen selection

READemption

A pipeline for the computational evaluation of RNA-Seq data

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python r bioinformatics rna-seq

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