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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

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