High-Throughput Biology - From Sequence to Networks Module 6 Lab

Generating a preqc report for the E. coli data set

# First build an FM-index of the two E. coli Illumina data sets:
sga index -t 4 -a ropebwt ecoli.illumina.15x.fastq
sga index -t 4 -a ropebwt ecoli.illumina.50x.fastq

# Next, we can run `sga preqc` to run the calculations and generate the PDF report.
sga preqc -t 4 ecoli.illumina.15x.fastq > ecoli.illumina.15x.preqc
sga preqc -t 4 ecoli.illumina.50x.fastq > ecoli.illumina.50x.preqc
python sga-preqc-report.py ecoli.illumina.15x.preqc ecoli.illumina.50x.preqc

Assembling the Oxford Nanopore Data

canu gnuplotTested=true -p ecoli-nanopore-canu -d ecoli-nanopore-auto genomeSize=4.6m -nanopore-raw ecoli.nanopore.25x.fasta