https://github.com/johandahlberg/awesome-10x-genomics

List of tools and resources related to the 10x Genomics GEMCode/Chromium system
https://github.com/johandahlberg/awesome-10x-genomics

List: awesome-10x-genomics

10x-genomics bioinformatics genomics

Last synced: 3 months ago
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List of tools and resources related to the 10x Genomics GEMCode/Chromium system

• Host: GitHub
• URL: https://github.com/johandahlberg/awesome-10x-genomics
• Owner: johandahlberg
• License: other
• Created: 2017-06-20T08:13:41.000Z (over 7 years ago)
• Default Branch: master
• Last Pushed: 2019-02-08T08:52:09.000Z (almost 6 years ago)
• Last Synced: 2024-05-23T02:02:24.474Z (8 months ago)
• Topics: 10x-genomics, bioinformatics, genomics
• Homepage:
• Size: 24.4 KB
• Stars: 85
• Watchers: 9
• Forks: 13
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.md

Awesome Lists containing this project

• awesome-linked-reads - Awesome-10x-genomics
• awesome-awesomeness-bioinformatics - Awesome 10x Genomics

README

        
Awesome 10x Genomics

====================

![10x genomics logo](10x_Genomics_Logo.png)

This repository attempts to gather tools related to the GEMCode/Chromium platforms from [10x Genomics](https://www.10xgenomics.com).

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](https://github.com/bcgsc/arcs) -

Scaffold genome sequence assemblies using linked read data

* [Athena](https://github.com/abishara/athena_meta) -

Read cloud assembler for metagenomes

* [BarCrawler](https://github.com/J35P312/BarCrawler) -

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

* [bxtools](https://github.com/walaj/bxtools) -

Tools for analyzing 10x data

* [EMerAld](http://cb.csail.mit.edu/cb/ema/) -

Fast and accurate alignment of barcoded short-reads

* [grocsvs](https://github.com/grocsvs/grocsvs) -

Genome-wide reconstruction of complex structural variants

* [LRSIM](https://github.com/aquaskyline/LRSIM) -

A simulator for linked reads

* [NAIBR](https://github.com/raphael-group/NAIBR) -

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

* [Samovar](https://github.com/cdarby/samovar) -

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

* [tenx_utils](https://github.com/friend1ws/tenx_utils) -

Utility functions for 10x data

* [Tigmint](https://github.com/bcgsc/tigmint) -

Correct misassemblies using Linked Reads

* [Topsorter](https://github.com/hanfang/Topsorter) -

Graphic assement of structural variants

* [scaff10x](https://sourceforge.net/projects/phusion2/files/scaff10x/) -

Scaffolding assemblies using linked read data

* [SuperNova](https://github.com/10XGenomics/supernova) -

10x Genomics Linked-Read Diploid De Novo Assembler

* [SVenX](https://github.com/vborjesson/SVenX) -

Pipeline for SV detection using 10X genomics data

Single cell

-----------

* [monocle-release](https://github.com/cole-trapnell-lab/monocle-release) -

R analysis toolkit for single cell genomics

* [seurat](https://github.com/satijalab/seurat) -

R toolkit for single cell genomics

* [Scanpy](https://github.com/theislab/scanpy) -

Toolkit for simulating and analyzing single cell data

* [TENxGenomics](https://github.com/mtmorgan/TENxGenomics) -

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

* [10xQC](http://10xqc.com/) -

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

* [VarTrix](https://github.com/10XGenomics/vartrix) -

Single-Cell Genotyping tool