312 Open source projects that are alternatives of or similar to bxtools

Multilocus sequence typing by blast using the schemes from PubMLST

Rapid large-scale prokaryote pan genome analysis

Antimicrobial Resistance Identification By Assembly

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

A collection of scripts and notes related to genomics and bioinformatics

A package for designing compact and comprehensive capture probe sets.

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

Genomics Extension for SQLite

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

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

Finds SNP sites from a multi-FASTA alignment file

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

Intuitive local web frontend for the BLAST bioinformatics tool

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

Data intensive science for everyone.

Analysis pipelines for sequencing data

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

Assembling the cause of phenotypes and genotypes from NGS data

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

An interactive web tool for quality control of DNA sequencing data

Official code repository for GATK versions 4 and up

A tool to circularize genome assemblies

Collection of scripts for bacterial genomics

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

Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data

Bioconductor package for management of multi-assay data

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

Nextflow basic tutorial for newbie users

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

Framework for Metastatic And Clonal History INtegrative Analysis

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

Big Compute Learning Labs

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

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.

Resource of human chromosome schematics & images

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

gargammel is an ancient DNA simulator

A library for manipulating bioinformatics sequencing formats in Apache Spark

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

Cloud-based single-cell copy-number variation analysis tool

Forward-time simulation in Python using fwdpp

A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

🐳 Bio-dockers: dockerized bioinformatic tools

Explore rearrangements and copy-number amplifications in a cancer genome

phenol: Phenotype ontology library

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

Maximum likelihood demultiplexing

Bead-based single-cell atac processing

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.

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

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

Numerical Encoding for Human Genetic Variants

Explore gnomAD datasets on the web

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

Identify phage regions in bacterial genomes for masking purposes

Ultrafast sequence typing and gene detection from NGS raw reads

FASTQ compression

Sequence lineage information extracted from RKI sequence data repo