569 Open source projects that are alternatives of or similar to Awesome 10x Genomics

A wrapper for the EnsEMBL REST API

MMseqs2: ultra fast and sensitive search and clustering suite

Introduction to Cloud Computing for Genomics

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

Real-time species-typing visualisation for nanopore data.

Genotyping of segregating mobile elements insertions

MyGene.info: A BioThings API for gene annotations

The START App: R Shiny Transcriptome Analysis Resource Tool

A tutorial on methods of 16S analysis with QIIME 1

MetaSRA: normalized sample-specific metadata for the Sequence Read Archive

Workflow Description Language - Specification and Implementations

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.

GO enrichment with python -- pandas meets networkx

A modular annotation tool for genomic variants

Detection of NCLDV signatures in 'omic data

pythonic wrapper for htslib

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Clustering scRNAseq by genotypes

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

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

The uncompromising Snakemake code formatter

Learn interpretable computational phenotyping models from k-merized genomic data

JAMP - Just Another Metabarcoding Pipeline

Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.

A D library for computational biology and bioinformatics

Grammar of Scalable Linked Interactive Nucleotide Graphics

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Tools for analyzing 10X Genomics data

ImmuneDB - A system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data

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.

an implementation of NSGA-II in java

Resource of human chromosome schematics & images

📦 🐳 Dockerfiles and documentation on tools for public health bioinformatics

A fast, scalable, and accurate local ancestry method.

VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.

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

DOM Text Based Multiple Sequence Alignment Library

A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

Data and analysis for the Splatter paper

Command line utility for manipulating Illumina-generated FastQ files.

MMseqs2 app to run on your workstation or servers

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

d3 library to build circular graphs

Read DNA sequences from colourful Microsoft Word documents

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

Phylogenetic trees in Julia

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

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

Identify phage regions in bacterial genomes for masking purposes

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

EpiViz is a scientific information visualization tool for genetic and epigenetic data, used to aid in the exploration and understanding of correlations between various genome features.

Spark VCF data source implementation for Dataframes

igv.js server and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"

Bioinformatics containers

Per-base per-nucleotide depth analysis

Genomics data visualization in Python by using matplotlib.

Comprehensive toolkit for generating various numerical features of protein sequences

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

A computational library for learning and evaluating biological knowledge graph embeddings

Highly customizable, ambiguity-aware dotplots for visual sequence analyses