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B-UMMI / DEN-IM

Dengue virus genotyping from shotgun and targeted metagenomics​ - A nextflow pipeline
GNU General Public License v3.0
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Feed in fasta files? #6

Closed tthye1 closed 3 years ago

tthye1 commented 3 years ago

Hello,

we have Dengue sequences (POLY gene) analysed by Sanger sequencing. Is it possible to feed in these fasta files into your pipeline, omitting the NGS part of the analysis?

Best wishes,

Thorsten

cimendes commented 3 years ago

Hello!

Currently, LMAS only accepts short-read sequencing data, either paired-end or single-end. At the moment we've no plans to allow complete FASTA DENV sequences to be passed for serotyping and genotyping, and multiple-sequence alignment as the NGS analysis component is an essential part to obtain accurate, reproducible and high-quality DENV sequences.

Thank you for your interest in LMAS!

cimendes commented 3 years ago

Closing due to lack of activity! If you have further questions please feel free to re-open this issue.