280 Open source projects that are alternatives of or similar to ipyrad

A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.

A library for manipulating bioinformatics sequencing formats in Apache Spark

GCModeller: genomics CAD(Computer Assistant Design) Modeller system in .NET language

Ultrafast sequence typing and gene detection from NGS raw reads

Nextflow basic tutorial for newbie users

pythonic wrapper for libhts (moved to: https://github.com/quinlan-lab/hts-python)

phenol: Phenotype ontology library

Tidy Verbs for Dealing with Genomic Data Frames https://const-ae.github.io/tidygenomics/

CUT&RUN and CUT&Tag data processing and analysis

Spark VCF data source implementation for Dataframes

DISCOVER co-occurrence and mutual exclusivity analysis for cancer genomics data

Bioconductor package for management of multi-assay data

Detection of evolutionary shifts in Ornstein-Uhlenbeck models

Big Compute Learning Labs

A fast, scalable, and accurate local ancestry method.

Forward-time simulation in Python using fwdpp

Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation

Explore gnomAD datasets on the web

MindTheGap is a SV caller for short read sequencing data dedicated to insertion variants (all sizes and types). It can also be used as a local assembly tool.

Manhattan plot Generator

Identify phage regions in bacterial genomes for masking purposes

Introduction to the Command Line for Genomics

A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

A bioinformatics API and web-app to integrate multi-omics datasets & interface with public databases.

WebAssembly modules for genomics

simple viewer for variant call format using htslib

Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.

R package: Simulate Expression data from igraph network using mvtnorm (CRAN; JOSS)

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

find large indels (in the blind spot between GATK/freebayes and SV callers)

Python-based UCSC genome browser snapshot-taker and gallery-maker

Framework for Metastatic And Clonal History INtegrative Analysis

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

A package for designing activity-informed nucleic acid diagnostics for viruses.

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

Multilocus sequence typing by blast using the schemes from PubMLST

Explore rearrangements and copy-number amplifications in a cancer genome

A tool to plot significant regions of GWAS

Bead-based single-cell atac processing

🐳 Bio-dockers: dockerized bioinformatic tools

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

An R framework for phylostratigraphy

Examples to get started with IBM Functional Genomics Platform

Numerical Encoding for Human Genetic Variants

Analysing Capture Seq Count Data

Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data

TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C

Consensus calling (or "reference assisted assembly"), chiefly of ancient mitochondria

Predict AMPs in (meta)genomes and peptides

ntHash implementation in Rust

simplified searching, fetching, and parsing records from NCBI using their E-utilities interface

A Snakemake workflow to process single samples or cohorts of paired-end sequencing data (WGS or WES) using trim galore/bwa/GATK4/parabricks.

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

GA4GH Variation Representation Python Implementation

Bioinformatics workflows developed for and used on the St. Jude Cloud project.

Grammar of Scalable Linked Interactive Nucleotide Graphics

Tools for analyzing 10X Genomics data

Resource of human chromosome schematics & images

Command line utility for manipulating Illumina-generated FastQ files.