569 Open source projects that are alternatives of or similar to staramr

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

🔬 BEDOPS: high-performance genomic feature operations

Ten Quick Tips for Deep Learning in Biology

Reads simulator

nim wrapper for htslib for parsing genomics data files

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

Assembling the cause of phenotypes and genotypes from NGS data

A curated list of awesome bioinformatics software.

Provide R access to the NCI Genomic Data Commons portal.

BACNET is a Java based platform to develop website for multi-omics analysis

Earl Grey: A fully automated TE curation and annotation pipeline

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

A tool to circularize genome assemblies

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

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

A comprehensive tutorial about GWAS and PRS

annotate a VCF with other VCFs/BEDs/tabixed files

Ultra-fast and memory-efficient (meta-)genome assembler

Java utilities for Bioinformatics

Python library to facilitate genome assembly, annotation, and comparative genomics

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

Python and C++ code for reading and writing genomics data.

Scripts to download genomes from the NCBI FTP servers

Tools to process and analyze deep sequencing data.

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Compute N50/NG50 and auN/auNG

Code examples of fast and simple k-mer counters for tutorial purposes

A fast whole-genome aligner based on de Bruijn graphs

An interactive web tool for quality control of DNA sequencing data

List of tools and resources related to the 10x Genomics GEMCode/Chromium system

Flexible genotype query among 30,000+ samples whole-genome

Antimicrobial Resistance Identification By Assembly

GCP Essentials for Bioinformatics Researchers

A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)

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

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

Rapid large-scale prokaryote pan genome analysis

cython + htslib == fast VCF and BCF processing

Haplotype VCF comparison tools

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

Chanjo provides a better way to analyze coverage data in clinical sequencing.

An interactive web portal for exploring immuno-oncology data

A modular annotation tool for genomic variants

Environmental DNA metabarcoding taxonomic identification

MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets

Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.

pythonic wrapper for htslib

InterARTIC - An interactive local web application for viral whole genome sequencing utilising the artic network pipelines..

Implementation of Neural Distance Embeddings for Biological Sequences (NeuroSEED) in PyTorch (NeurIPS 2021)

Clustering scRNAseq by genotypes

A proof of concept of RNAseq pipeline

Version 5 of the CAFE phylogenetics software

Complex structural variant detection from WGS data

Command line tool to run batch jobs concurrently with ETL framework on AWS or other cloud computing resources

Monorepo with JBrowse 2 web, JBrowse 2 desktop, the JB core package, and core plugins. To customize behaviors, write an in-house plugin.

TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.

Streamlining SLAM-seq analysis with ultra-high sensitivity

A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using coalescent and concatenation approaches