VirusMap is my first attempt at a computational biology analysis tool. It is built using snakemake. I tried using Magic-Blast to look for reads in the SRA, but the connection is not stable for searching large datasets. VirusMap will download reads and map locally. Aligment is performed by SRA with a specifc target genome. I'll probally go back to Magic-Blast for more general local searches.
First clone this repo...
$ bash setup.sh
Set SRA_IDS, VIRAL_GENBANK_IDS and ALIGNERS in config.js
$ snakemake
config can also be specified from the command line:
$ snakemake --config SRA_IDS="SRR1553459" VIRAL_GENBANK_IDS="NC_002549" ALIGNERS="minimap2"
A tested dataset can be run with:
$ snakemake --config TESTING=true
$ snakemake -p --latency-wait 60 --cluster "qsub -v PATH='<path_to_miniconda_bin>:$PATH' -d <outdir> -o <outdir>/qsublogs/ -e <outdir>/qsublogs/ -l mem={params.mem} -l nodes=1:ppn={threads}" -j 25
- Curl is backup
- Fasta-dump freaked out and downloaded 32Gb of data instead of the 4Gb reads...
- Biopython - it's python
- FASTQC
- Trim Galore!
- STAR doesn't work well on datasets that contain a bunch of reads that don't map.
- Maybe Magic-Blast locally?
- bwa mem has some trouble with the pair-end-reads...
- minimap2 looks good so far...
- Qualimap
- MultiQC
The ncbi has a good SnakeMake tutorial https://nbis-reproducible-research.readthedocs.io/en/latest/snakemake/