219 Open source projects that are alternatives of or similar to recentrifuge

Reference-based transcript discovery from long RNA read

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.

Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).

A package for designing compact and comprehensive capture probe sets.

SARS-CoV-2 workflow for nanopore sequence data

NGLess: NGS with less work

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

Official code repository for GATK versions 4 and up

🔬 De novo assembly of nanopore reads using nextflow

PEPPER-Margin-DeepVariant

Transposon Insertion Finder - Detection of new insertions in NGS data

RNA-seq workflow using STAR and DESeq2

A small python program to simulate a real-time Nanopore sequencing run based on a previous experiment.

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

Long read / genome alignment software

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

A fast tool for hybrid genome assembly of long and short reads

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

Fast-SG: An alignment-free algorithm for ultrafast scaffolding graph construction from short or long reads.

A versatile sequenced read processor for nanopore direct RNA sequencing

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

Data intensive science for everyone.

Tools to process and analyze deep sequencing data.

Nanopore demultiplexing, QC and alignment pipeline

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

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

Tools for working with genomic and high throughput sequencing data.

Pipeline for annotating genomes using long read transcriptomics data with pinfish

R package for analyzing single-cell RNA-seq 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.

UGENE is free open-source cross-platform bioinformatics software

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

Sequana: a set of Snakemake NGS pipelines

Predict plasmids from uncorrected long read data

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

An accurate and ultra-fast hybrid genome assembler

ABRA2

Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing

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

Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data

Estimation of per-individual inbreeding coefficients under a probabilistic framework

MaAsLin2: Microbiome Multivariate Association with Linear Models

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

A curated list of awesome nanopore analysis tools.

Estimation of pairwise distances under a probabilistic framework

VBZ compression plugin for nanopore signal data

C library for high-throughput sequencing data formats

Research release basecalling models and configurations

Java utilities for Bioinformatics

Classify sequencing reads using MinHash.

A simplified pipeline for ctDNA sequencing data analysis

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

A tool to identify, orient, trim and rescue full length cDNA reads

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.

Project metadata manager for PEPs in Python

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

A collection of Galaxy-related training material

A tool for analysis of assembly graphs

Real-time species-typing visualisation for nanopore data.