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. 2022 Dec 17;26(1):105815. doi: 10.1016/j.isci.2022.105815
REAGENT or RESOURCE SOURCE IDENTIFIER
Biological samples
Sphyrna mokarran (female) tissues: heart Nova Southeastern University; Conservation Biology Laboratory OC-313
Isurus oxyrinchus (male) tissues: liver, muscle, heart Nova Southeastern University; Conservation Biology Laboratory OC-298
Deposited data
Sphyrna mokarran assembly This paper NCBI:JAGIQG010000000
Sphyrna mokarran raw reads (Pacbio) This paper SRA: SRR20233585
Sphyrna mokarran raw reads (Illumina) This paper SRA: SRR20233586
Sphyrna mokarran RNA-seq (Illumina) Marra et al.,51 2017 (PMID: 28132643) SRA: SRR3213610
Isurus oxyrinchus assembly This paper NCBI: JANJGN010000000
Isurus oxyrinchus raw reads (Pacbio) This paper SRA: SRR20231275
Isurus oxyrinchus raw reads (Illumina) This paper SRA: SRR20823548, SRR20823549, SRR20823550, SRR20823551, SRR20823552
Isurus oxyrinchus RNA-seq liver (Pacbio Iso-seq) This paper SRA: SRR20245707
Isurus oxyrinchus RNA-seq muscle (Pacbio Iso-seq) This paper SRA: SRR20245706
Isurus oxyrinchus RNA-seq heart (Illumina) Marra et al.51 2017 (PMID: 28132643) SRA: SRR3213609
Genome annotation gff files for Sphyrna mokarran and Isurus oxyrinchus assemblies This paper https://doi.org/10.5061/dryad.mgqnk992h
Software and algorithms
MaSuRCA v3.3.3 Zimin et al.,52 2017 https://github.com/alekseyzimin/masurca
Hifiasm v0.14 Cheng et al.,53 2021 https://github.com/chhylp123/hifiasm
Maker v2.31 Holt and Yandell,56 2011 https://www.yandell-lab.org/software/maker.html
Augustus v3.3.3 Stanke et al.79 2008 https://github.com/Gaius-Augustus/Augustus
Trinity v2.10.0 Haas et al.,57 2013 https://github.com/trinityrnaseq/trinityrnaseq/
PASA v2.4.1 Haas et al.,58 2003 https://sourceforge.net/projects/pasa/
EVidenceModeler v1.1.1 Haas et al.,59 2008 https://sourceforge.net/projects/evidencemodeler/
BUSCO v5.1.2 Seppey et al.,63 2019 https://busco.ezlab.org/
Stringtie2 v1.3.6 Kovaka et al.,61 2019 https://github.com/skovaka/stringtie2
TAMA Kuo et al.,62 2019 https://github.com/GenomeRIK/tama
BLAST2GO Götz et al.,64 2008 https://www.blast2go.com/
picard v 2.26.1 Picard,70 2019 https://broadinstitute.github.io/picard/
GATK v 3.8.1 https://gatk.broadinstitute.org/hc/en-us
VCFtools v 0.1.17 Danecek et al.78 2011 http://vcftools.sourceforge.net/
samtools. v 1.15.1 Danecek et al.,71 2021 http://www.htslib.org/
bedmap v 2.4.35 https://doi.org/10.1093/bioinformatics/bts277
psmc v 0.6.5 Durbin and Li,28 2011 https://github.com/lh3/psmc
R v 4.1.2 https://www.r-project.org/
Rstudio 2021.09.0 https://www.rstudio.com/
Trimmomatic v 0.39 Bolger et al.,69 2014 https://bioweb.pasteur.fr/packages/pack@Trimmomatic@0.39
BWA-MEM v0.7.17 Li,65 2013 https://guix.gnu.org/packages/bwa-0.7.17/