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cfe-lab / MiCall

Pipeline for processing FASTQ data from an Illumina MiSeq to genotype human RNA viruses like HIV and hepatitis C
https://cfe-lab.github.io/MiCall
GNU Affero General Public License v3.0
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MiCall for data on NextSeq/iSeq? plus other questions #1200

Open ammaraziz opened 4 days ago

ammaraziz commented 4 days ago

Hi CFE-Lab,

We (VIDRL) are moving from sanger sequencing to HTS sequencing using a custom hybridisation probe panel which will be sequenced on either iSeq or NextSeq. I've looked at a few pipelines, with MiCall being the (IMO) the one which ticks all the boxes. I had a few questions if you had sometime to answer:

  1. Can MiCall be used on different illumina platforms?
  2. From reading the code, the pipeline isn't tied to your internal systems (eg on Kive) and it can be deployed on any system?
  3. I want to confirm MiCall is doing the resistance interpretation locally and not using the Sierra API to transmit data to stanford?

Thanks!

Ammar

donkirkby commented 3 days ago

We've only used it on MiSeq data, but its only critical dependency is on the FASTQ file format. You should be able to work around differences in any other dependencies, like the Interop folder data. MiCall doesn't need to run under Kive, you can run it under docker, run it under Singularity, run it on BaseSpace, or install the dependencies and run it directly on your system.

We're happy to give guidance if you have any questions as you try to run it on your own data.