tseemann/nullarbor

Query: Mixed sample - separate reads?

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#267 opened on Jun 3, 2020

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Description

Hi,

I'm not sure if this is possible but thought I would ask. I am working with mycobacteria and one of our samples is a mixed sample. I believe Karken can determine if samples are mixed and was wondering does it pick it up when you run Nullarbor? I am currently running a few samples to see. If it does, can you separate the reads? is it possible to separate reads in a mixed sample?

Cheers for any advice/tips!

P

Contributor guide

Research direction
Check the Nullarbor documentation and source code for features related to mixed sample detection and read separation. Look for command line options like contaminant or mixed, and review the pipeline steps that involve Kraken.
Tech stack
perl
Domain
bioinformatics
Issue type
Research
DifficultyEstimated implementation difficulty for a new contributor, from 1 for very small changes to 5 for expert-level work.
2
Estimated timeA rough time range for an experienced contributor to investigate, implement, test, and prepare a pull request.
Under 1 hour
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Active
ClarityHow clearly the issue explains the expected change, acceptance criteria, and next step.
Clear
Prerequisites
GitBioinformatics
Newbie friendlinessA 1-100 score estimating how approachable this issue is for first-time contributors.
75