====== SOAPdenovo2 Update ======

====Second pass at adapter trimming====
  * 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

====Second pass Musket error correction====
  * 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

====Assembly runs====
===Runtime stats===
  * 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
===Results from run 1===
==Contigs:==
  * 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%)
==Scaffolds:==
  * 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%)