Awesome 10x Genomics

This repository attempts to gather tools related to the GEMCode/Chromium platforms from 10x Genomics.

How to contribute

Contribute to this repo by creating a PR with one or more new tools, and a link(s) to the corresponding repo(s) and a short description of what the tool does.

Linked reads

• arcs - Scaffold genome sequence assemblies using linked read data

• Athena - Read cloud assembler for metagenomes

• BarCrawler - An easy to use QC package for 10X genomics barcoded reads.

• bxtools - Tools for analyzing 10x data

• EMerAld - Fast and accurate alignment of barcoded short-reads

• grocsvs - Genome-wide reconstruction of complex structural variants

• LRSIM - A simulator for linked reads

• NAIBR - Identifies novel adjacencies created by structural variation events such as deletions, duplications, inversions, and complex rearrangements

• Samovar - Somatic (mosaic) SNV caller for 10X Genomics data using random forest classification and feature-based filters

• tenx_utils - Utility functions for 10x data

• Tigmint - Correct misassemblies using Linked Reads

• Topsorter - Graphic assement of structural variants

• scaff10x - Scaffolding assemblies using linked read data

• SuperNova - 10x Genomics Linked-Read Diploid De Novo Assembler

• SVenX - Pipeline for SV detection using 10X genomics data

Single cell

• monocle-release - R analysis toolkit for single cell genomics

• seurat - R toolkit for single cell genomics

• Scanpy - Toolkit for simulating and analyzing single cell data

• TENxGenomics - R interface to the 1.3 M single cell data set from 10x Genomics

• 10xQC - Database of 10x single cell QC metrics submitted by research groups worldwide

• VarTrix - Single-Cell Genotyping tool