Closed karthick1087 closed 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
Great!!, thank you for the information.
@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 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!!!!
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.