333 Open source projects that are alternatives of or similar to bio-dockers

Data intensive science for everyone.

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

Official code repository for GATK versions 4 and up

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

A package for designing compact and comprehensive capture probe sets.

NGLess: NGS with less work

A library for manipulating bioinformatics sequencing formats in Apache Spark

Tools to process and analyze deep sequencing data.

Java utilities for Bioinformatics

MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.

Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.

Ultrafast sequence typing and gene detection from NGS raw reads

A Java API for high-throughput sequencing data (HTS) formats.

Collection of scripts for bacterial genomics

CUT&RUN and CUT&Tag data processing and analysis

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

No description or website provided.

Consensus calling (or "reference assisted assembly"), chiefly of ancient mitochondria

Transcripts annotation and GO enrichment Fisher tests

Improve the quality of a denovo assembly by scaffolding and gap filling

My bioinfo toolbox

A bioinformatics API and web-app to integrate multi-omics datasets & interface with public databases.

Explore rearrangements and copy-number amplifications in a cancer genome

A Snakemake workflow to process single samples or cohorts of paired-end sequencing data (WGS or WES) using trim galore/bwa/GATK4/parabricks.

GA4GH Variation Representation Python Implementation

Spark VCF data source implementation for Dataframes

Bioconductor package for management of multi-assay data

Exome/Capture/RNASeq Pipeline Implementation using snakemake

Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding

Analysing Capture Seq Count Data

Big Compute Learning Labs

A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

Bioinformatics workflows developed for and used on the St. Jude Cloud project.

Introduction to the Command Line for Genomics

DISCOVER co-occurrence and mutual exclusivity analysis for cancer genomics data

TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C

ntHash implementation in Rust

Forward-time simulation in Python using fwdpp

A method for circular DNA detection based on probabilistic mapping of ultrashort reads

Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.

simple viewer for variant call format using htslib

phenol: Phenotype ontology library

A secure encryption tool for genomic data

Numerical Encoding for Human Genetic Variants

Large genome reassembly based on Hi-C data, continuation of GRAAL

Bead-based single-cell atac processing

use the noise

The GenePattern Server web application

myVCF: a web-based platform for target and exome mutations data management

Explore gnomAD datasets on the web

DriverPower

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

Multi-sample somatic variant caller

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

simplified searching, fetching, and parsing records from NCBI using their E-utilities interface

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies

LRSDAY: Long-read Sequencing Data Analysis for Yeasts

mity: A highly sensitive mitochondrial variant analysis pipeline for whole genome sequencing data