Compare alignment rates

Compare alignment rates

This recipe compares alignment before and after QC using two different tools, bwa and bowtie2

0 results • updated 5 weeks ago by Bioinformatics Admin • needs authorization

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.

Interesting cases

 # 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
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