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replikation / poreCov

SARS-CoV-2 workflow for nanopore sequence data
https://case-group.github.io/
GNU General Public License v3.0
39 stars 16 forks source link

Illumina support #151

Closed karthick1087 closed 3 years ago

karthick1087 commented 3 years ago

Hi, The tool is great. Can we use for Illumina paired end/Iontorrent PGM data as well. It will be helpful if it is extended to this two second generation platform starting from basecalled fastq reads to mutation profiling.

replikation commented 3 years ago

hi, its only available for nanopore data. however, it is possible to provide genomes from e.g. a Illumina-based assembly. (to generate the overview report) (via the --fasta flag) a ready to use illumina pipeline can be found here for instance (https://gitlab.com/RKIBioinformaticsPipelines/ncov_minipipe) also containerized. hope this helps

karthick1087 commented 3 years ago

Great!!, thank you for the information.

hoelzer commented 3 years ago

@karthick1087 yes exactly and as @replikation stated already you might want to give https://gitlab.com/RKIBioinformaticsPipelines/ncov_minipipe a try, developed specifically for Illumina data. The default usage here is currently Snakemake+Conda and not Nextflow+Docker but we also provide a single Docker image if needed.

And we will continue to develop this pipeline for Illumina in the next months as well.

karthick1087 commented 2 years ago

@karthick1087 yes exactly and as @replikation stated already you might want to give https://gitlab.com/RKIBioinformaticsPipelines/ncov_minipipe a try, developed specifically for Illumina data. The default usage here is currently Snakemake+Conda and not Nextflow+Docker but we also provide a single Docker image if needed.

And we will continue to develop this pipeline for Illumina in the next months as well.

Thank you for the information. I tried the tool. Working well!!!!