| Biological samples |
|
| Ossabaw pig |
This study |
NA |
|
| Deposited data |
|
| Sequencing data for Ossabaw pig |
This study |
CNGB Sequence Archive (https://db.cngb.org/cnsa/) under the accession number CNP0001681 |
| Genome assembly for Ossabaw pig |
This study |
CNGB Sequence Archive (https://db.cngb.org/cnsa/) under the accession number CNA0020809 |
|
| Software and algorithms |
|
| SOAPfilter v2.2 |
(Luo et al., 2012) |
https://github.com/aquaskyline/SOAPdenovo2 |
| Supernova v2.11 |
(Weisenfeld et al., 2017) |
https://support.10xgenomics.com/de-novo-assembly/software/downloads/latest |
| Redundans |
(Pryszcz and Gabaldón, 2016) |
https://github.com/lpryszcz/redundans |
| stLFR_GapCloser |
BGI-Qingdao |
https://github.com/BGI-Qingdao/stLFR_GapCloser |
| Pilon v1.2.3 |
(Walker et al., 2014) |
https://github.com/broadinstitute/pilon/releases/ |
| TGS-GapCloser |
(Xu et al., 2019) |
https://github.com/BGI-Qingdao/TGS-GapCloser |
| RaGOO v1.1 |
(Alonge et al., 2019) |
https://github.com/malonge/RaGOO |
| RepeatMasker v4.0.5 |
(Tarailo-Graovac and Chen, 2009) |
http://www.repeatmasker.org/ |
| RepeatModeler v1.0.8 |
(Tarailo-Graovac and Chen, 2009) |
http://www.repeatmasker.org/RepeatModeler/ |
| LTR-FINDER v1.0.6 |
(Xu and Wang, 2007) |
https://github.com/oushujun/LTR_FINDER_parallel |
| Tandem Repeat Finder v4.0.7 |
(Benson, 1999) |
https://tandem.bu.edu/trf/trf.html |
| BLAT v36 |
(Kent, 2002) |
https://genome.ucsc.edu/cgi-bin/hgBlat?command=start |
| GeneWise v2.4.1 |
(Birney et al., 2004) |
https://www.ebi.ac.uk/∼birney/wise2/ |
| Augustus v3.1 |
(Keller et al., 2011) |
http://augustus.gobics.de/ |
| EVidenceModeler v1.1.1 |
(Haas et al., 2008) |
https://evidencemodeler.github.io/ |
| BUSCO v2.0 |
(Simao et al., 2015) |
https://busco-archive.ezlab.org/v2/ |
| BLAST v2.2.26 |
(Altschul et al., 1990) |
https://blast.ncbi.nlm.nih.gov/Blast.cgi |
| BWA-MEM v0.7.12 |
(Li and Durbin, 2010) |
https://github.com/lh3/bwa |
| SAMtools v0.1.19 |
(Guindon et al., 2009) |
https://github.com/samtools/samtools |
| Picard package v1.54 |
Broad Institute |
https://broadinstitute.github.io/picard/ |
| GATK v4.1.2 |
(McKenna et al., 2010) |
https://gatk.broadinstitute.org/hc/en-us |
| PSMC v0.6.5 |
(Li and Durbin, 2011) |
https://github.com/lh3/psmc |
| TreeFam v1.1 |
(Li et al., 2006) |
http://www.treefam.org/ |
| CAFÉ v2.1 |
(De Bie et al., 2006) |
https://github.com/hahnlab/CAFE |
| PAML v4.9 |
(Yang, 2007) |
http://abacus.gene.ucl.ac.uk/software/paml.html |
| MUSCLE v3.8.31 |
(Edgar, 2004) |
https://www.ebi.ac.uk/Tools/msa/muscle/ |
| PRANK v100802. |
(Löytynoja, 2014) |
https://www.ebi.ac.uk/research/goldman/software/prank |
| gBlocks v0.91b |
(Talavera and Castresana, 2007) |
https://github.com/atmaivancevic/Gblocks |
| LastZ v1.1 |
(Harris, 2007) |
http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.02.00/README.lastz-1.02.00a.html |
| Smartie-sv |
(Kronenberg et al., 2018) |
https://github.com/zeeev/smartie-sv |
| SOAPnuke v1.6.5 |
(Chen et al., 2017) |
https://github.com/BGI-flexlab/SOAPnuke |
| Bowtie2 |
(Langmead and Salzberg, 2012) |
https://github.com/BenLangmead/bowtie2 |
| RSEM v1.2.31 |
(Li and Dewey, 2011) |
https://github.com/deweylab/RSEM |
