• Trimming was performed using Skewer on the initial datasets SW019_S1/S2 and SW018_S1, all the read sets that were sequenced at UCSC.
• Used fastqc to confirm adapter presence in reads, primarily in SW018 reads, overrepresented sequence matched adapter sequence.
• Effective adapter trimming confirmed with another fastqc run.
• Compared Skewer results to results from SeqPrep (without merging) and found nearly identical results

• Used the second pass adapter-trimmed data, and a kmer size of 31
• Observed no big differences in kmer spectra compared to previous Musket run

• Did two runs, both with the adapter-trimmed, error-corrected reads described above. First run mis-specified the orientation of one library (reads were specified as ←- –> instead of –> ←-), second run corrected this error in the config file.
• Split into four steps, sparse pregraph construction, contig generation, mapping, and scaffold generation.
• Sparse pregraph: 37.8 CPU hours and 60 GB max virtual memory for 1st run || 35.4 CPU hours and 60 GB max virt memory for 2nd run
• Contig generation: 0.23 CPU hours and 5.8 GB max virt memory for 1st run || 0.24 CPU hours and 5.8 GB max virt memory for 2nd run
• Mapping: 21.9 CPU hours and 66 GB max virt memory for 1st run || 14.8 CPU hours and 78 GB max virt memory for 2nd run
• Scaffold generation: 92.7 CPU hours and 20 GB max virt memory for 1st run || Still in progress for 2nd run



• Total contig sequence size : 2,051,251,797
• Contig count : 3,854,379
• Mean length : 532
• Longest sequence : 22,512
• N50 : 1,425 ; count : 389,550
• length > 1K : 583,671 (15.14%)
• length > 10K : 891 (0.02%)

• Total assembly size (including ‘N’s) : 2,064,665,199
• Total assembly size (without ‘N’s) : 1,974,393,478
• Scaffold count : 2,030,303
• Mean length : 1,016
• Longest sequence : 60,333
• N50 : 5,554 ; count : 105,217
• length > 1K : 381,668 (18.80%)
• length > 10K : 35,884 (1.77%)