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CFSAN-Biostatistics / shigatyper

CFSAN Shigella Typing Pipeline
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Non-Illumina reads #2

Closed AntonMatiiv closed 1 year ago

AntonMatiiv commented 4 years ago

Hi! Is it possible to use shigatyper for non-Illumina reads? For example, MGISEQ reads.

florathecat commented 4 years ago

Hi Anton, Thanks for your message. shigatyper reads paired-end fastq files so I imagine it should read MGISEQ reads. However if you only have single-end reads the script needs to be tweaked.

AntonMatiiv commented 4 years ago

Thank you very much for your answer!

rpetit3 commented 2 years ago

Hi @AntonMatiiv

v2 of Shigatyper now supports Single-end and Nanopore reads

Cheers