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

Spatial transcriptomics

• FlashDeconv -
  High-performance spatial transcriptomics deconvolution for Visium HD and other 10x platforms. Processes 1M spots in ~3 minutes.

• Squidpy -
  Spatial single cell analysis in Python, builds on scanpy and anndata

• cell2location -
  Bayesian model for mapping fine-grained cell types in spatial transcriptomics