Dear IDseq dev team,
First of all, thank you for creating this pipeline. It has so far been fantastic and I truly think it will make metagenomic sequencing far more accessible to researchers around the world who struggle with the bioinformatics.
Having tested the pipeline for almost 2 months now, I think addition of the following features would be helpful for all users:
1. Ability to move files across projects.
Reasoning: by mistake, I ended up uploading some files to the wrong project. Rather than having to re-upload those files to the correct project (which also wastes significant amount of computational time in to re-process in the pipeline), would be great if we can transfer files that are "complete" to the correct project folder.
2. Ability to select multiple files within the project - either through drag of a mouse cursor OR keyboard short-cut.
Reasoning: When a project folder contains hundreds of files, selecting just a subset to delete (if they only partially uploaded and need to re-upload, or has failed in the pipeline for some reason) or to generate heatmaps from is VERY tedious and time consuming, clicking samples one by one.
3. When exporting the heatmaps via .csv, export with the settings selected (e.g. positivity threshold).
Reasoning: It is great that we can set positivity thresholds based on read counts per million, read number (NT/NR), etc. and view it graphically straight away online as a heatmap. However, when exported into .csv, the current output just gives the raw read counts without any thresholds applied. This means, I need to re-apply manually such thresholds. Just would make life easier to export with thresholds applied.
4. When exporting at species level, is it possible to also have the respective genus name exported together? The family and actual genbank accession name also would be good to have in additional columns.
Reasoning: Sometimes when the positive "hit" reads have a species name but genus not specified (likely to be when reference genome was added to NCBI), these read counts "disappear" when the heatmap is exported at genus level. Having the respective genus name in the species level export of .csv, would make it easier to confirm this.
5. Ability to export the contig mapping results - the .bam or .sam files.
Reasoning: Without these files, I end up needing to re-run mapping analyses myself to get alignment stats like average coverage per nucleotide, etc.
Once again, a big thank you and keep up the fantastic work! Look forward to seeing more improvements in the future and hopefully have the above features added soon.
JDRF International Postdoctoral Fellow
UNSW Medicine, School of Women’s and Children’s Health
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