petersm3 / filterfastq Goto Github PK

Create a demo to be quickly run, e.g., provide:

• PhiX reference genome
• Small FASTQ file with PhiX contaminate
• bash script to run the pipeline with a summary of the results

Would need to potentially retool the script to ensure it can pickup the blastn binary by default

Need to call $split variable on https://github.com/petersm3/filterfastq/blob/main/filterfastq.pl#L211 instead of picking it up from $PATH

Update https://github.com/petersm3/filterfastq/blob/main/filterfastq.pl#L67 to check $fastq_to_fasta