76 Open source projects that are alternatives of or similar to BWA-MEME

ABRA2

Estimation of pairwise distances under a probabilistic framework

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

Sequana: a set of Snakemake NGS pipelines

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

An easy-to-use way for running Galaxy workflows.

Estimation of per-individual inbreeding coefficients under a probabilistic framework

My bioinfo toolbox

Java utilities for Bioinformatics

A collection of Galaxy-related training material

UGENE is free open-source cross-platform bioinformatics software

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

Metagenomics/viromics pipeline that focuses on automation, user-friendliness and a clear audit trail. Jovian aims to empower classical biologists and wet-lab personnel to do metagenomics/viromics analyses themselves, without bioinformatics expertise.

TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models

Ultrafast sequence typing and gene detection from NGS raw reads

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

Rare variant test software for next generation sequencing data

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

A library for manipulating bioinformatics sequencing formats in Apache Spark

C library for high-throughput sequencing data formats

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

A simplified pipeline for ctDNA sequencing data analysis

An automated RNA-seq pipeline using Nextflow

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

Tools for working with genomic and high throughput sequencing data.

NGLess: NGS with less work

is an open-source LIMS (laboratory Information Management System) for Next Generation Sequencing sample management, statistics and reports, and bioinformatics analysis service management.

A course on Analysing Next Generation (/High Throughput etc..) Sequencing data using Bioconductor

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

A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies

Dockerised Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation)

Parallel Sequence to Graph Alignment

A method for variant graph genotyping based on exact alignment of k-mers

myVCF: a web-based platform for target and exome mutations data management

Official code repository for GATK versions 4 and up

A workflow for creating small NGS test data sets, useful for continuous integration.

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

No description or website provided.

Transposon Insertion Finder - Detection of new insertions in NGS data

Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.

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

Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay

Data intensive science for everyone.

Customizable workflows based on snakemake and python for the analysis of NGS data

Tools to process and analyze deep sequencing data.

A method for circular DNA detection based on probabilistic mapping of ultrashort reads

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

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

DNAscan is a fast and efficient bioinformatics pipeline that allows for the analysis of DNA Next Generation sequencing data, requiring very little computational effort and memory usage.

Exome/Capture/RNASeq Pipeline Implementation using snakemake

Project metadata manager for PEPs in Python

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

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

Collection of scripts for bacterial genomics

RNA-seq workflow using STAR and DESeq2

Utilities for analyzing next generation sequencing data.

🐳 Bio-dockers: dockerized bioinformatic tools

Multi-sample somatic variant caller

RNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data.

R package for analyzing single-cell RNA-seq data