/awesome-10x-genomics

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

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Awesome 10x Genomics

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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