1173 Open source projects that are alternatives of or similar to bac-genomics-scripts

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

Ultrafast sequence typing and gene detection from NGS raw reads

A package for designing compact and comprehensive capture probe sets.

Data intensive science for everyone.

Official code repository for GATK versions 4 and up

A collection of scripts and notes related to genomics and bioinformatics

UGENE is free open-source cross-platform bioinformatics software

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

NGLess: NGS with less work

Java utilities for Bioinformatics

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

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

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

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

Tools for analyzing 10X Genomics data

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

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.

An easy-to-use way for running Galaxy workflows.

Tools to process and analyze deep sequencing data.

Analysis pipelines for sequencing data

Antimicrobial Resistance Identification By Assembly

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

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

A tool to circularize genome assemblies

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

Finds SNP sites from a multi-FASTA alignment file

PHANOTATE: a tool to annotate phage genomes.

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

A library for manipulating bioinformatics sequencing formats in Apache Spark

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

Multilocus sequence typing by blast using the schemes from PubMLST

🐳 Bio-dockers: dockerized bioinformatic tools

Clustering scRNAseq by genotypes

HTS-compatible wrapper for IgBlast V-(D)-J mapping tool

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

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

A collection of publications on comparison of high-throughput sequencing technologies.

Assembling the cause of phenotypes and genotypes from NGS data

Genomics Extension for SQLite

An interactive web tool for quality control of DNA sequencing data

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

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

A scalable bacterial genome assembly, annotation and analysis pipeline

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

annotate a VCF with other VCFs/BEDs/tabixed files

A comprehensive tutorial about GWAS and PRS

🎓Repository for university labs on FAMCS, BSU

Analysing Capture Seq Count Data

Intuitive local web frontend for the BLAST bioinformatics tool

GenomeTools genome analysis system.

STAPLE (Shared Tools for Automatic Personalised Lower Extremity modelling) consists of a collection of methods for generating skeletal models from three-dimensional bone geometries, usually segmented from medical images. The methods are currently being expanded to create complete musculoskeletal models.

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

A repository for setting up a RNAseq workflow

Generate duplex/single consensus reads to reduce sequencing noises and remove duplications

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

Rapid large-scale prokaryote pan genome analysis

Toolbox for deep, resilient, markup-invariant linking into HTML documents without their cooperation

xHLA: Fast and accurate HLA typing from short read sequence data

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