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

A fast 23andMe genome text file parser, now superseded by arv

Bayesian genotyper for structural variants

The next version of bwa-mem

Scripts to download genomes from the NCBI FTP servers

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

An interactive web tool for quality control of DNA sequencing data

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

A curated list of bioinformatics bench-marking papers and resources.

Efficient pythonic random access to fasta subsequences

A collection of scripts and notes related to genomics and bioinformatics

Rapid large-scale prokaryote pan genome analysis

Ten Quick Tips for Deep Learning in Biology

Earl Grey: A fully automated TE curation and annotation pipeline

A powerful open source data warehouse system

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

Proof-of-concept seq-to-graph mapper and graph generator

GenomeTools genome analysis system.

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

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

cython + htslib == fast VCF and BCF processing

A genome browser that shows long reads and complex variants better

A faster lmm for GWAS. Supports GPU backend.

A simple command-line tool to download data from Joint Genome Institute databases

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

Haplotype VCF comparison tools

Simple pure Python SAM parser and objects for working with SAM records

Elastic, reproducible, and reusable genomic data science tools from R backed by cloud resources

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

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

Bystro genetic analysis (annotation, filtering, statistics)

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

Assembling the cause of phenotypes and genotypes from NGS data

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

Genomics Extension for SQLite

Fast alignment and preprocessing of chromatin profiles

A curated list of awesome bioinformatics software.

Compute N50/NG50 and auN/auNG

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

A comprehensive tutorial about GWAS and PRS

A versatile pairwise aligner for genomic and spliced nucleotide sequences

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

Pan-genome wide association studies

A Practical and Efficient NCBI Taxonomy Toolkit

SquiggleKit: A toolkit for manipulating nanopore signal data

EDAM is an ontology of bioinformatics types of data including identifiers, data formats, operations and topics.

variant expressions, annotation, and filtering for great good.

GO enrichment with python -- pandas meets networkx

SortMeRNA: next-generation sequence filtering and alignment tool

MyGene.info: A BioThings API for gene annotations

Application for making ENCODE Blacklists

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.

Biological sequences for the julia language

Simulate genealogical trees and genomic sequence data using population genetic models

Provides access to complex Bioinformatics software (even BioLinux!) in just one command.

Protein-Level ASSembler (PLASS): sensitive and precise protein assembler

A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)

Robust and efficient workflows using a simple language agnostic approach

The START App: R Shiny Transcriptome Analysis Resource Tool