108 Open source projects that are alternatives of or similar to Shasta

Data intensive science for everyone.

A collection of scripts and notes related to genomics and bioinformatics

A package for designing compact and comprehensive capture probe sets.

UGENE is free open-source cross-platform bioinformatics software

Analysis pipelines for sequencing data

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

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.

FluentDNA allows you to browse sequence data of any size using a zooming visualization similar to Google Maps. You can use FluentDNA as a standalone program or as a python module for your own bioinformatics projects.

16,432 Free Yara rules created by

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

Fast and accurate sequence demultiplexing

Simple & Efficient data access for Scala and Scala.js

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

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

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

RNASeq pipeline

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

NexusTK DAT Object Viewer

Double Sided Assembly Line Balancing with Genetic Algorithm (C#)

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

Antimicrobial Resistance Identification By Assembly

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

DNA sequence viewer supporting custom, GenBank, FASTA, NCBI accession, and iGEM input.

Fast and flexible ORF finder

A python-based isomiR quantification and analysis pipeline

parallelized blat with multi-threads support

3d engine implementation in DNA code!

Discovering known and novel miRNAs from small RNA sequencing data

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design

Efficient pythonic random access to fasta subsequences

ABRA2

Nucleotide Archival Format - Compressed file format for DNA/RNA/protein sequences

A fast 23andMe genome text file parser, now superseded by arv

Polyrhythmic Sequencer library for Web Audio API.

highly-efficient & lightweight mutation signature matrix aggregation

COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)

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

Validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.

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

A curated list of awesome bioinformatics software.

Rapid large-scale prokaryote pan genome analysis

Assembling the cause of phenotypes and genotypes from NGS data

Predicting Future Influenza Virus Sequences with Machine Learning

Genomics Extension for SQLite

A python wrapper for the benchling api

😴 📂 Create and Query a Local Copy of GenBank in R

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

Precision HLA typing from next-generation sequencing data

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

Structural variant toolkit for VCFs

Visualizing DNA Sequences via Javascript

tools for working with genome variation graphs

🚀 A sequencing simulator

minimalistic nucleic acid folding

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

Analysis Pipeline for Single Cell ATAC-seq

A repository for setting up a RNAseq workflow