This recipe compares alignment before and after QC using two different tools, bwa and bowtie2
Requirements the bioinfo environment and:
pip bio install --upgrade
Download the recipe and run it at command line:
bash Compare_alignment_rates.sh CP050134 SRR653447
The first parameter is the SRR accession number the second number is the GenBank id for the reference genome.
# Ebola virus, bwa better by default
bash Compare_alignment_rates.sh AF086833 SRR1972739
# Zika virus Bowtie works better by default
bash Compare_alignment_rates.sh KY075939 SRR5122835
# Tobacco etch virus genome
bash Compare_alignment_rates.sh NC_001555 SRR3466599
# The alignment is worse after trimming! Whoops!
bash Compare_alignment_rates.sh VWSY01000001 SRR16249304
If you want to know more about each sample run:
bio search AF086833 SRR1972739