Oly Genome Comparison
Sam has compiled the current status of Olympia oyster genome assemblies here. I am going to try to assess differences.
Metassembler approach seemed not to produce anything.
Canu which is PacBio only, created a fasta post Pilon polishing.
Redundans was used on Illumina and PacBio. 2 runs. Try 2 seemed better. will take
D-173-250-161-130:NewOlyAssembly Sean$ assembly-stats scaffolds.reduced.fa stats for scaffolds.reduced.fa sum = 546928670, n = 300593, ave = 1819.50, largest = 78788 N50 = 3852, n = 36149 N60 = 2917, n = 52500 N70 = 2137, n = 74420 N80 = 1455, n = 105359 N90 = 810, n = 155023 N100 = 200, n = 300593 N_count = 5238187 Gaps = 209203
Taking “BGI” scaffolds and renaming
Here is what we have
791MB Sep 8 08:10 ol-bgisoap-161129.fa 48MB Sep 8 07:49 ol-canu-170623.fa 558MB Sep 8 07:52 ol-redundans-170608.fa
to that lets add what we have been using
Ostrea_lurida-Scaff-10k.fa (131.4 MB)
Running some bsmap ie
!/Applications/bsmap-2.74/bsmap \ -a zr_1-sub001.fastq \ -d ol-bgisoap-161129.fa \ -o /Volumes/Monarch/wd/17-09-08/bsmap_out_soap-2.sam \ -p 4 \ 2> /Volumes/Monarch/wd/17-09-08/stderr_bsmap_soap-2.txt
results are as follows
ol-bgisoap-161129.fa - 3.1% aligned reads ol-canu-170623.fa - 12% aligned reads ol-redundans-170608.fa - 2.3% aligned reads Ostrea_lurida-Scaff-10k.fa - 6% aligned reads
Canu looks good. Would like to know exactly how that was derived. Will go ahead and crunch data with Canu- but will examine metaassemblers to see if we can get Canu (PacBio) and Illumina assembly combined.