Wednesday Warmup Exercise

Align E. coli reads (PacBio) to E. coli Reference

Let’s align some PacBio reads from the E. coli K12, MG1655 strain to an E. coli K12, MG1655 reference genome. If you google for “Koren MG1655 wgs-assembler” you should find this page, where three xzipped fastq files can be downloaded. Grab just one, and uncompress it. Then, grab the appropriate reference genome (as we did yesterday). Finally, take only the first ~4000 reads from the read set, and align them to the reference, to produce a SAM file, as we did yesterday. Does everything look as expected?