Index of /public/2025Q1

 Name                     Last modified      Size  Description
 Parent Directory                              -   
 SeaOtter/                2025-02-20 07:47    -   
 Rockfish/                2025-02-20 07:47    -   
 CAFlannelBush/           2025-02-20 07:47    -   
 seqkit.hifiasm.stats.tsv 2025-02-23 14:23  2.8K  
 README.txt               2025-02-23 14:54  1.4K  

OVERVIEW
    This directory includes whole genome sequencing datasets generated on Revio and Vega systems
    for California flannelBush, widow rockfish, and sea otter and associated hifiasm assemblies. 
    
    Samples were provided by the California Conservation Genomics Project (CCGP). 
    Thanks to the CCGP including Erin Toffelmier, Brad Shaffer, Oanh Nguyen, Courtney Miller, 
    Merly Escalona, and Lutz Froenicke.


METHODS
    SAMPLES         California flannelbush (Fremontodendron californicum)
                    Widow rockfish (Sebastes entomelas)
                    Sea otter (Enhydra lutris)
    LIBRARY PREP    SMRTbell libraries provided by CCGP; SMRTbell prep kit 3.0
    SEQUENCING      Vega system, Vega chemistry, 24 hour movie
                    Revio system, SPRQ chemistry, 24 hour movie
    ANALYSIS        Subsampled Revio data to ~65 Gbp HiFi yield (no subsample for Vega), 
                    convert uBAM to FASTQ, assemble with hifiasm v0.24.0-r702

# Subsample data to ~65 Gbp (for Revio data only)
samtools view -@ 64 -s <SUBSAMP%> -b MOVIE.hifi_reads.bam > SPECIES.revio.downsamp.bam
pbindex -j 64 SPECIES.revio.downsamp.bam

# Convert uBAM to FASTQ
bam2fastq -u -j 16 -o SPECIES.revio.downsamp SPECIES.revio.downsamp.bam
pigz -9 -p 16 SPECIES.revio.downsamp.fastq

# Run hifiasm v0.24.0-r702
hifiasm -t 64 -o SPECIES.asm SPECIES.revio.downsamp.fastq.gz