483 Open source projects that are alternatives of or similar to Migmap

A package for designing compact and comprehensive capture probe sets.

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

Official code repository for GATK versions 4 and up

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

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

Data intensive science for everyone.

UGENE is free open-source cross-platform bioinformatics software

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

highly-efficient & lightweight mutation signature matrix aggregation

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

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

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

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

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

(No maintenance) OpenGene, core libraries for NGS data analysis and bioinformatics in Julia

Structural variant toolkit for VCFs

An interactive web tool for quality control of DNA sequencing data

Genomics Extension for SQLite

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

A tool to circularize genome assemblies

Antimicrobial Resistance Identification By Assembly

NGLess: NGS with less work

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

Rapid large-scale prokaryote pan genome analysis

Intuitive local web frontend for the BLAST bioinformatics tool

Collection of scripts for bacterial genomics

(No maintenance) Detect gene fusion directly from raw fastq files

An NGS read trimming tool that is specific, sensitive, and speedy. (production)

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

Method to optimally select samples for validation and resequencing

C library for high-throughput sequencing data formats

Tools for working with genomic and high throughput sequencing data.

R package for analyzing single-cell RNA-seq data

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

A robust model for quantitative comparison of ChIP-Seq data sets.

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

Analysis pipelines for sequencing data

Project metadata manager for PEPs in Python

A collection of scripts and notes related to genomics and bioinformatics

A simplified pipeline for ctDNA sequencing data analysis

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

A repository for setting up a RNAseq workflow

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

Assembling the cause of phenotypes and genotypes from NGS data

Java utilities for Bioinformatics

Tools to process and analyze deep sequencing data.

(formerly eelpond) an automated RNA-Seq workflow system

Comprehensive toolkit for generating various numerical features of protein sequences

UNCURL is a tool for single cell RNA-seq data analysis.

JAMP - Just Another Metabarcoding Pipeline

an implementation of NSGA-II in java

Estimation of per-individual inbreeding coefficients under a probabilistic framework

DEPRECIATED! Please use nf-core/tools instead

Data and analysis for the Splatter paper

GeneValidator: Identify problems with predicted genes

R scripts to reproduce analyses in our paper comparing clustering methods for high-dimensional cytometry data

Single-Cell Analysis in Python. Scales to >1M cells.

A Python package for fast operations on 1-dimensional genomic signal tracks

A full spaCy pipeline and models for scientific/biomedical documents.

Estimation of pairwise distances under a probabilistic framework