IN NCBI and COGE- Released- PacBio CLR data

Jamaican Lion Female (mother) Assembly

https://mega.nz/#!1BYRyKDK!zOlM1xdGMAAoqk9z0vLmrTKFdf3UlhLjPUr9-Kp-kgA

Jamaican Lion Male (father) Assembly

https://mega.nz/#!AZJDQQ4K!3EVfai2DSa22cOeBvmG4f5Ph729xE66pNMXavK0SXVs

Jamaican Lion F1 (daughter) Assembly

https://mega.nz/#!ZcRlhAZJ!u2RQwYdS_Kx3qMLdzsim_kA_iWoY3rCv7P2Dpr6ru3I

Jamaican Lion Mother + Y Assembly

Jamaican Lion Female + Y NCBI

 

Mother Annotation

https://mega.nz/#!1cJ1QYBD!-Y33wOcJVJ8ZvM_XSxA7qxy15i7PurvNQRZu0ygEDjw

Father Annotation

https://mega.nz/#!pBYBjIbI!ph_afATKUVkmJCdNqKJgpTJ3dTj7CxdGwexoenmdKuA

Excel sheet describing THCAS, CBDAS, CBCAS

https://mega.nz/#!NNI1VKSa!BxUNtyke7eB4esMy9sy1JYbE_Qon0RhoZWQPpjggQbw

 

Sequence and annotation of 42 cannabis genomes reveals extensive copy number variation in cannabinoid synthesis and pathogen resistance genes

PAG 2020 presentations on this topic and Future Directions.

What constitutes a good reference?

How do we move beyond a single reference. Pan Genomes require new assembly tools

Jamaican Lion HIFI CannAssemblethon

(Warning… These are draft assemblies)

20kb HiFi Library was sequenced on Sequel II.

Peregrine Assembly (Jason Chin)

Completed in 7 hours on an 64Gb MacOS with 1Tb of flash storage.

Alt Haplotigs https://mega.nz/#!5JIQlIoS!Urfqrc3WcIZor8XZkC4aCjHpamkXILQdBIGApb5YnEU

Primary Assembly

https://mega.nz/#!VYQCSAib!eOKs27Yg1ab-2on92ZeaADfcWM7jhstTIARIpB0l0OE

Quast analysis of Peregrin Assembly
BUSCO analysis of Primary Assembly

HiCanu Assembly (Sergey Koren)

Primary Assembly

https://mega.nz/#!8IITTCpY!MSfL9h5icwjhTb0Y4FIKv0f2n648uQ4R2_xChoAZmAs

Alternative Assembly

https://mega.nz/#!1YQVwQbB!BEzwP07yvz8FzHUtI_2_LO4f1lDVMYUS4_aNvci-ZD4

Merged Assembly (ASM)

https://mega.nz/#!4RBhGYwI!0kEI9wDW5ooHjgiQRJGfItO_3PqZz0R2kEWzbgl7p3U

Quast evaluation of HiCanu Primary Assembly
BUSCO evaluation of Primary assembly shows low duplication rate.
BUSCO scores from the merged assembly have high duplication rates but also the highest completion. Important to note that CBDAS and THCAS ended up in the Alt Assembly.

HiFiAsm (Greg Concepcion & Heng Li)

Primary and Alt Assembly as one Tar.gz

https://mega.nz/#!FEQViSpL!7-_09OBKmdNro-CKdeMlMcHx-QCa3ZZOsxs1itfGFCE

HiAsm BUSCO scores. BUSCO run by G.Concepcion may be more recent version than above.

FALCON- UNZIP (G.Concepcion)

Various FALCON assemblies with differing Unzip stringencies
Phased blocks in the genome

Selected 99.97% Primary Assembly

https://mega.nz/#!RERgHYTT!i4EN3i23ypK3MnV4cusJIIM7Uf-Up3OL-IwsAIq_XsQ

Phase Genomics Hi-C data.

Forward Read (30Gb) & Reverse Read (30Gb).

https://mega.nz/file/QIJCSSRb#W80B2ct56kXCD7NlVsaJp3EC5n60Ts24Ub-e3pLEppE

https://mega.nz/file/gUJz3QDZ#PiODeEipI2hLol10peqdwKD76kxLOz8zJFnPfdincPs

HiCanu HIC Files

https://mega.nz/file/dRpHwKwY#1Qs0sL6s-JI8JMxZcOhKLkJaeESY2hKMZ3m0whPu7I8

CLR Jamaican Lion Assembly in NCBI as of 2020: HIC File.

https://mega.nz/file/gVZUnChZ#yNouUHhUCrFSe-9BKve78_YyXr5elmQVl2n4mn8Gbas

SALSA mapping of Reads on HiCanu Assembly of HiFi data with 2020 Phase Genomics data
Current Assembly in NCBI CLR assembly. 2020 Phase Genomics data.

In May of 2020, Heng Li updated HiFiASM to purge duplicate haplotigs. This produce an 8.6Mb N50 assembly with BUSCO scores over 97.3%

Jamaican Lion Mother ONT data (14Gb zipped)

https://mega.nz/file/RJA1mK4J#M8rIxc8j4Yl7VOYcIYcl_G8Ye8DrjbMkKKu-XhJ2Vo8