74 Open source projects that are alternatives of or similar to ginkgo

Official code repository for GATK versions 4 and up

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

Rapid large-scale prokaryote pan genome analysis

An interactive web tool for quality control of DNA sequencing data

parallelized blat with multi-threads support

Intuitive local web frontend for the BLAST bioinformatics tool

A python-based isomiR quantification and analysis pipeline

CellRank for directed single-cell fate mapping

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

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

Polyrhythmic Sequencer library for Web Audio API.

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.

A Python library for creating and manipulating musical patterns, designed for use in algorithmic composition, generative music and sonification. Can be used to generate MIDI events, MIDI files, OSC messages, or custom events.

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

Callable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer

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

De novo assembly from Oxford Nanopore reads.

Data intensive science for everyone.

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

Fast and accurate sequence demultiplexing

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

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

HMMRATAC peak caller for ATAC-seq data

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

UGENE is free open-source cross-platform bioinformatics software

Genomics Extension for SQLite

Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)

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

Structural variant toolkit for VCFs

Basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files

Discovering known and novel miRNAs from small RNA sequencing data

Sampler, Sequencer, Multi-engine synth and effects - in a box! [WIP]

Analysis pipelines for sequencing data

Differential abundance (DA) and correlation analyses for microbial absolute abundance data

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

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

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

<<------ Use SnapATAC!!

highly-efficient & lightweight mutation signature matrix aggregation

Analysis Pipeline for Single Cell ATAC-seq

Simple & Efficient data access for Scala and Scala.js

Maximum likelihood demultiplexing

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

A repository for setting up a RNAseq workflow

RNASeq pipeline

A deep learning-based tool for alignment and integration of single cell genomic data across multiple datasets, species, conditions, batches

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

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

Assembling the cause of phenotypes and genotypes from NGS data

Finds SNP sites from a multi-FASTA alignment file

A package for designing compact and comprehensive capture probe sets.

A tool to circularize genome assemblies

🚀 A sequencing simulator

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

A collection of scripts and notes related to genomics and bioinformatics

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

FASTQ compression

Collection of scripts for bacterial genomics

Indigo: SNV and InDel Discovery in Chromatogram traces obtained from Sanger sequencing of PCR products

Antimicrobial Resistance Identification By Assembly