hsmurali / scrapt Goto Github PK

Hi there,

I browsed your interesting paper (that isnt mentioned in the README) and was intrigued by the speed improvement while promising a similar performance compared to DADA2. I'd like to ask whether you are going to add the tool to bioconda, that would make it available as conda package and container (bioconda packages are also available as docker & singularity containers). Packaging & containerization would make the tool even more useful by using the package/container instead of going through an installation procedure. This allows efficient use in pipelines and makes analyses reproducible.

Small side questions: the README states

  -f FILEPATH, --filepath FILEPATH
                        Path to the file containing 16S sequences. At the
                        moment we support only fatsa file containing the 16S
                        reads.

• is that fasta file, as in not fastq?
• Path to the file containing 16S sequences. = Path to raw sequencing read file in fasta format.?
• what about multiple samples and therefore multiple raw sequencing read files?
• will it only work for 16S rRNA amplicon sequencing data or also any other amplicon (I would expect the latter, but that isnt reflected in the README)

Best, Daniel