4781 Open source projects that are alternatives of or similar to Sequenceserver

Data intensive science for everyone.

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

Analysis pipelines for sequencing data

Official code repository for GATK versions 4 and up

Genomics Extension for SQLite

An interactive web tool for quality control of DNA sequencing data

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

Rapid large-scale prokaryote pan genome analysis

A tool to circularize genome assemblies

Antimicrobial Resistance Identification By Assembly

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

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

SaffronTree: Reference free rapid phylogenetic tree construction from raw read 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

A package for designing compact and comprehensive capture probe sets.

A collection of scripts and notes related to genomics and bioinformatics

Assembling the cause of phenotypes and genotypes from NGS data

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

Scalable genomic data analysis.

highly-efficient & lightweight mutation signature matrix aggregation

Efficient variant-call data storage and retrieval library using the TileDB storage library.

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

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

Flexible genotype query among 30,000+ samples whole-genome

A fast whole-genome aligner based on de Bruijn graphs

List of tools and resources related to the 10x Genomics GEMCode/Chromium system

Python and C++ code for reading and writing genomics data.

Scripts to download genomes from the NCBI FTP servers

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

Tools to process and analyze deep sequencing data.

A powerful open source data warehouse system

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

Conda recipes for the bioconda channel.

Bioinformatics library for .NET

GCP Essentials for Bioinformatics Researchers

Bayesian genotyper for structural variants

Model and predict short DNA sequence features with neural networks

Structural variant toolkit for VCFs

📖🔬☕️ BioJava is an open-source project dedicated to providing a Java library for processing biological data.

NGLess: NGS with less work

A cool place to store your Hi-C

UGENE is free open-source cross-platform bioinformatics software

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

Code examples of fast and simple k-mer counters for tutorial purposes

A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)

nim wrapper for htslib for parsing genomics data files

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

Bayesian haplotype-based mutation calling

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

A repository for setting up a RNAseq workflow

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary

Ten Quick Tips for Deep Learning in Biology

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

Reads simulator

Deep learning infrastructure for bioinformatics

Python library to facilitate genome assembly, annotation, and comparative genomics

The next version of bwa-mem