de-novo analysis

NeutronStar is a bioinformatics best-practice analysis pipeline used for de novo assembly and quality-control of 10x Genomics Chromium data. The pipeline is built using Nextflow, and comes with docker / singularity containers to make the results highly reproducible.

nf-core/neutronstar

https://github.com/nf-core/neutronstar

De novo assembly pipeline for 10X linked-reads using Supernova - https://nf-co.re/neutronstar

When we run analysis

We run this analysis by request for all de novo projects where we have prepared the sequencing library in-house. If you have prepared a library yourself and we are just sequencing, please get in touch and mention that you would like us to run this analysis.

Input data

Reads sequenced from 10X Genomics’ Chromium Genome libraries. It is recommended that they are sequenced to around 60X nominal genome coverage. For a primer on how to obtain the best results for a typical Chromium de novo project, please refer to this document.

Results

There are two outputs from the Supernova assembler included, a ‘pseudohaploid’ representation and a ‘diploid’ representation where blocks of contiguously called haplotypes are outputted as two separate sequences. Additional assembly evaluation is performed using QUAST and BUSCO.

Please note that the output from this pipeline is a first-draft assembly. That means additional curation is always recommended, e.g. gap-filling and haplotig removal.

Applications
Method Status

Pilot

We are currently testing this method. Please contact us to find out more.

Keywords