Building a workflow in CLC Genomics Workbench for AMR prediction Video
There's been a lot of chatter about bioinformatics workflow in peer publications and in social media recently - so I thought I'd show how workflows are supported in QIAGEN Bioinformatics' CLC Genomics Workbench. In this short 2 minute (accelerated) video, you'll see a workflow being built in CLC from scratch for analysis of antimicrobial resistance in microbiome data. The workflow includes quality control, trimming, metagenomics de novo assembly, gene finding, functional gene prediction, contig binning by both taxonomic and sequence characteristics, identification of antimicrobial resistance genes, assembly free analysis of reads likely to have AMR markers, and mapping of reads back to binned contigs. The output is a series of reports from each tool, and a BED tools like track visualization of reads mapped to AMR positive contigs.
It was a lot of fun to create. Took about 10-15 minutes to build (i know what to look for of course), and about 30m to run on my 16GB mem laptop. Funny thing was it took longer to get the audio right than it did to build and run the analysis. 😂