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.
Renaming oly_polished_.fasta to ol-canu-170623.fa
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
renaming scaffolds.reduced.fa to ol-redundans-170608.fa
Taking “BGI” scaffolds and renaming ol-bgisoap-161129.fa.
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.