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Genome Assemblies

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kubu4 edited this page May 14, 2021 · 14 revisions
sequence_ID sequencer(s) assembly_url(fasta) assembler(s) reference initials date notebook_url
pbjelly_sjw_01 pacbio/illumina 20171130_oly_pbjelly/jelly.out.fasta pbjelly BGI sjw 20171130 https://robertslab.github.io/sams-notebook/2017/11/30/genome-assembly-olympia-oyster-illumina-pacbio-using-pb-jelly-wbgi-scaffold-assembly-2.html
redundans_sjw_03 pacbio/illumina 20171024_docker_oly_redundans_01/scaffolds.reduced.fa reduands/canu canu_sjw_01 sjw 20171024 http://onsnetwork.org/kubu4/2017/10/24/genome-assembly-olympia-oyster-illumina-pacbio-reads-using-redundans/
redundans_sjw_02 pacbio/illumina 20171004_redundans/scaffolds.reduced.fa redundans/canu canu_sb_01 sjw 20171006 http://onsnetwork.org/kubu4/2017/10/06/genome-assembly-olympia-oyster-redundanscanu-vs-redundansracon/
redundans_sjw_01 pacbio/illumina 20171005_redundans/scaffolds.reduced.fa redundans/racon racon_sjw_01 sjw 20171006 http://onsnetwork.org/kubu4/2017/10/06/genome-assembly-olympia-oyster-redundanscanu-vs-redundansracon/
redundans_sb_02 pacbio/illumina Oly_Redundans_Output_Try_2/scaffolds.reduced.fa redundans/canu canu_sb_01 sb 20170608 https://genefish.wordpress.com/2017/06/08/seans-notebook-oly-genome-re-assembly-try-2/
redundans_sb_01 pacbio/illumina Oly_Redundans_Output/scaffolds.reduced.fa redundans/canu canu_sb_01 sb 20170524 https://genefish.wordpress.com/2017/05/24/oly-genome-redundans-run-finished/
racon_sjw_01 pacbio 20170918_oly_pacbio_racon1_consensus.fasta racon NA sjw 20170918 http://onsnetwork.org/kubu4/2017/09/18/genome-assembly-olympia-oyster-pacbio-minimapminiasmracon-3/
canu_sjw_01 pacbio 20171018_oly_pacbio.contigs.fasta canu NA sjw 20171018 http://onsnetwork.org/kubu4/2017/10/18/genome-assembly-olympia-oyster-pacbio-canu-v1-6/
canu_sb_01 pacbio oly_pacbio_.contigs.fasta canu NA sb 20170619 https://genefish.wordpress.com/2017/06/19/seans-notebook-canu-run-finished/
soap_bgi_01 illumina Ostrea_lurida.fa soap NA BGI 20161221 NA
platanus_sb_02 illumina Oly_Platanus_Assembly_Kmer-22/Oly_Out__contig.fa platanus NA sb 20170602 https://genefish.wordpress.com/2017/06/02/oly-assembly-try-2-its-yuuuuuuge/
platanus_sb_01 illumina Oly_Out__contig.fa platanus NA sb 20170519 https://genefish.wordpress.com/2017/05/19/seans-notebook-olympia-oyster-genome/

Quast Comparison of Assemblies (20180116)

See Sam's Notebook for specifics.

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Genome Assembly

2bRAD Sequencing

Genotype-by-sequencing

Genome Sequencing

Methylation Assessment

RNA-Seq

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