Available as bioconda package?

[d4straub]

Available as bioconda package?

[hsmurali]

Thank you! We don't have it on bioconda yet. We will seriously consider making it available as a bioconda package.

1. The current version of SCRAPT takes as input a fasta file since it assumes the sequences are preprocessed and quality filtered. We recommend using QIIME2 to preprocess sequences from all samples and multiplexing reads that pass the quality filter into a single fasta file.

2. SCRAPT takes sequences pooled from all samples as input. This is similar to the pooled mode of DADA2. We plan to provide a pipeline to perform preprocessing in the future iterations of SCRAPT. We also plan on providing a sample x OTU table that can be used for differential abundance testing in the future.

3. SCRAPT can be applied on any amplicon sequencing dataset and not just 16S rRNA. In the paper we present some results on 18S rRNA gene, which is a marker found in microeukaryotes.

Please feel free to reach out, if you have further queries on preprocessing raw read files.

Thank you.