I’m relatively new to genomic data management and am learning as I go. I have some Genome Skimming data and I’d like to map it to a concatenated gene sequence (from the HybSeq probes of GoFlag). Doing this in Geneious is straightforward because it just involves mapping and generating a consensus sequence. However, I haven’t found tools in Galaxy to do this. I’ve tried using BWA, Bowtie2, and HISAT2, but they produce SAM/BAM files, and I haven’t found a tool to generate the consensus sequence and align the data afterwards.
Or, navigate to a tool, and see if it is included in a tutorial. Example: SPAdes genome assembler for genomes of regular and single-cell projects → tool link at UseGalaxy.org → link to SPAdes tutorials
If I am understanding what you have done so far … you can extract the filtered reads (those that mapped) into fastq format with SamToFastq (from Samtools, accepts BAM), then assemble the reads, and do the downstream steps.
All of this can be done in Galaxy. From what I know about Geneious, some of the “tools” are actually mini workflows that group a few functions. You can create the same groupings in Galaxy, and add those to the tool panel as “custom tools” (favorite workflows), or group the entire process into a larger workflow. The tutorials above all have workflow templates to get you started, or you can exact a workflow from your history once you have the process worked out.
If you can’t find out what each step was actually doing in the other application, maybe find a publication that has the steps clearly defined, and work from that instead? If you share that, or the exact steps any other way, we can help to find those functions in Galaxy.
