404 Open source projects that are alternatives of or similar to polyRAD

R package for analyzing single-cell RNA-seq data

Biostar Q&A

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

Package for fetching metadata and downloading data from SRA/ENA/GEO

Versatile open-source tool for microbiome analysis

dysgu-SV is a collection of tools for calling structural variants using short or long reads

Workflow Description Language - Specification and Implementations

parallel fastq-dump wrapper

Fast motif matching in R

Tools and databases for analyzing HLA and VDJ genes.

A cross-platform command-line tool for executing jobs in parallel

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

The next version of bwa-mem

The BridgeDb Library source code

A modern genome browser built with JavaScript and HTML5.

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

Signal-level algorithms for MinION data

Compute N50/NG50 and auN/auNG

A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentation and downloading the program, please see the home page:

Cutadapt removes adapter sequences from sequencing reads

GNparser normalises scientific names and extracts their semantic elements.

Working with molecular structures in pandas DataFrames

nim wrapper for htslib for parsing genomics data files

Java utilities for Bioinformatics

CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)

Bioinformatics one liners from Ming Tang

Simple simulation of single-cell RNA sequencing data

A comprehensive tutorial about GWAS and PRS

A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment

Modular and universal bioinformatics

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

The Chemistry Development Kit

🐛 How to use CENTIPEDE to determine if a transcription factor is bound.

An open source platform for managing and analyzing biomedical big data

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

Structural variant and indel caller for mapped sequencing data

Toolkit for preparing genomes for submission to NCBI

A high-performance, Pythonic language for bioinformatics

🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results

A React web application to query and share any PostgreSQL database.

SIMD-accelerated library for computing global and X-drop affine gap penalty sequence-to-sequence or sequence-to-profile alignments using an adaptive block-based algorithm.

👁 Python library to plot DNA sequence features (e.g. from Genbank files)

Single cell perturbation prediction

Detecting methylation using signal-level features from Nanopore sequencing reads of plants

Computational Analysis of Novel Drug Opportunities

Highly adaptable common interface for proteomics search and de novo engines

Application for making ENCODE Blacklists

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

WebGL Heatmap Viewer for Big Data and Bioinformatics

dna2vec: Consistent vector representations of variable-length k-mers

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

exploratory and interactive microbiome analyses based on heatmaps

A curated list of awesome bioinformatics software.

Per-base per-nucleotide depth analysis

3D printed sculpture of a DNA molecule, showing my own genome

Open source Java library for computational proteomics

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).