# Red Sea Urchin (*Mesocentrotus franciscanus*) Genome

The genome assembly, annotations, and all raw data associated with this project are affiliated with NCBI BioProject PRJNA914702.


## Sample preparation information:

The organism used to generate this assembly was a male red sea urchin, samples ID "Mf1", with a 101 mm test diameter. DNA for all sequencing was extracted from gonad tissue following a modified CTAB extraction procedure (please reference publication for additional information).  
Dissections were done by Andrea Bodnar, and DNA extractions by Jennifer Polinski. 

## Illumina short-read library prep:

DNA was mechanically sheared to ~500 bp on a Covaris M220a and bead-cleaned/size-selected with PCRclean DX beads (Aline Biosciences) prior to library prep following manufacturer's SOP with the KAPA HyprePrep DNA kit (Roche). 1.5 ug of DNA went into the KAPA prep, a double-sides size selection targeting fragments 450-600 bp was done, and no PCR amplification steps were performed. The resulting library was sequenced at GMGI on a NextSeq 500 using a v2.5 high-output 2x150 kit.  
Illumina library prep and sequencing were done by Jennifer Polinski.

## ONT long-read sequencing:

Prior to ONT library prep, DNA was size-selected for large fragments using SPRI beads with custom buffers (buffer 1 = ONT "SPRI size selection protocol for >1.5-2 kb"  & Stortchevoi et al. 2020). DNA size distribution and quantity were determined using the Fragment Analyzer gDNA kit (Agilent) and Qubit dsDNA BR assay. 1 ug of HMW DNA was prepared for ONT sequencing with the NAnopore Ligation Sequencing Kit (SQK-LSK109) following manufacturer's specifications, and sequenced on a MinION sequencers. Four ONT library preps and sequencing runs were performed to achieve desired coverage.Basecaling was performed using ONT Guppy with the following command: ```ont-guppy-cpu/bin/guppy_basecaller -i ./fast5/ -s ./fastq/ -c /data/app/nanopore/ont-guppy-cpu/data/dna_r9.4.1_450bps_hac.cfg --num_callers 10```.   
ONT library prep and sequencing were done by Jennifer Polinski.

## Hi-C sequencing:

Hi-C libraries were generated by [Phase Genome](https://phasegenomics.com/) using gonad tissue from Mf1.  

## Genome assembly and analyses:

Information for each step of genome assembly and analysis can be found in the appropriate directory here, in the order listed.