87 Open source projects that are alternatives of or similar to HMMRATAC

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

Discovering known and novel miRNAs from small RNA sequencing data

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

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.

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

Genomics Extension for SQLite

A package for designing compact and comprehensive capture probe sets.

A repository for setting up a RNAseq workflow

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

Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.

gargammel is an ancient DNA simulator

Simple & Efficient data access for Scala and Scala.js

A collection of scripts and notes related to genomics and bioinformatics

RNASeq pipeline

Analysis Pipeline for Single Cell ATAC-seq

Assembling the cause of phenotypes and genotypes from NGS data

Structural variant toolkit for VCFs

🚀 A sequencing simulator

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

Tools for analyzing 10X Genomics data

Analysis pipelines for sequencing data

Framework for Metastatic And Clonal History INtegrative Analysis

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

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

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

FASTQ compression

Data intensive science for everyone.

UGENE is free open-source cross-platform bioinformatics software

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

De novo assembly from Oxford Nanopore reads.

Fast and accurate sequence demultiplexing

Antimicrobial Resistance Identification By Assembly

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

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.

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

Polyrhythmic Sequencer library for Web Audio API.

parallelized blat with multi-threads support

Rapid large-scale prokaryote pan genome analysis

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

An interactive web tool for quality control of DNA sequencing data

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

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

AStarix: Fast and Optimal Sequence-to-Graph Aligner

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

Sequence lineage information extracted from RKI sequence data repo

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

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

Official code repository for GATK versions 4 and up

Multilocus sequence typing by blast using the schemes from PubMLST

Intuitive local web frontend for the BLAST bioinformatics tool

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

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

Maximum likelihood demultiplexing

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 python-based isomiR quantification and analysis pipeline

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

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

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

A tool to circularize genome assemblies

highly-efficient & lightweight mutation signature matrix aggregation