280 Open source projects that are alternatives of or similar to barque

WebAssembly modules for genomics

Python-based UCSC genome browser snapshot-taker and gallery-maker

Tidy Verbs for Dealing with Genomic Data Frames https://const-ae.github.io/tidygenomics/

Identify phage regions in bacterial genomes for masking purposes

Bead-based single-cell atac processing

Resource of human chromosome schematics & images

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

Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.

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

Command line utility for manipulating Illumina-generated FastQ files.

GCModeller: genomics CAD(Computer Assistant Design) Modeller system in .NET language

Examples to get started with IBM Functional Genomics Platform

MindTheGap is a SV caller for short read sequencing data dedicated to insertion variants (all sizes and types). It can also be used as a local assembly tool.

Spark VCF data source implementation for Dataframes

Learn interpretable computational phenotyping models from k-merized genomic data

Transcripts annotation and GO enrichment Fisher tests

A fast, scalable, and accurate local ancestry method.

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

Monorepo with JBrowse 2 web, JBrowse 2 desktop, the JB core package, and core plugins. To customize behaviors, write an in-house plugin.

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.

A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

Explore rearrangements and copy-number amplifications in a cancer genome

Grammar of Scalable Linked Interactive Nucleotide Graphics

A fast tool for hybrid genome assembly of long and short reads

pythonic wrapper for libhts (moved to: https://github.com/quinlan-lab/hts-python)

🐳 Bio-dockers: dockerized bioinformatic tools

Manhattan plot Generator

A package for designing activity-informed nucleic acid diagnostics for viruses.

Numerical Encoding for Human Genetic Variants

Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing

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

Predict AMPs in (meta)genomes and peptides

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

A proof of concept of RNAseq pipeline

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

find large indels (in the blind spot between GATK/freebayes and SV callers)

An alternative to MCMC for rapid analysis of models

mgatk: mitochondrial genome analysis toolkit

Bioconductor package for management of multi-assay data

A tool to plot significant regions of GWAS

Nextflow basic tutorial for newbie users

InterARTIC - An interactive local web application for viral whole genome sequencing utilising the artic network pipelines..

Big Compute Learning Labs

Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data

A library for manipulating bioinformatics sequencing formats in Apache Spark

Interactive assembly and analysis of RAD-seq data sets

Forward-time simulation in Python using fwdpp

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

phenol: Phenotype ontology library

TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.

Explore gnomAD datasets on the web

R package: Simulate Expression data from igraph network using mvtnorm (CRAN; JOSS)

Ultrafast sequence typing and gene detection from NGS raw reads

An R framework for phylostratigraphy

Multilocus sequence typing by blast using the schemes from PubMLST

pythonic wrapper for htslib

Clustering scRNAseq by genotypes

A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using coalescent and concatenation approaches

Tools for analyzing 10X Genomics data

Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation