Great advice @gbbio!!
Then Hi @bacterial_dna – The only thing I would add is some technical help for that first step. Did the the sequencing center deliver the Illumina WGS reads in a BAM format to start? That is pretty common and getting the reads out into fastq datasets is a single step.
Search the tool panel at a UseGalaxy server (https://galaxyproject.org/ → Regions) with some keywords to find appropriate tools. Something like “bam to fastq”. Either of these are good choices. If one fails, try a different one, or try different settings. If you get errors, you can share back your history for more help.
- bedtools Convert from BAM to FastQ
- SamToFastq extract reads and qualities from SAM/BAM dataset and convert to fastq
The reads won’t be mapped yet, so the file is not really a full BAM yet but a special class of “read only BAM”. You want all the data to start with. One extracted, organize your reads, then QA and all the other downstream steps.
Hope this helps! 