Aspidoscelis tigris

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Resource Primary Assembly Alternate Assembly
GenBank rAspTig1: GCA_023333525.1 rAspTig1: GCA_023333555.1
ENA rAspTig1: GCA_023333525.1 rAspTig1: GCA_023333555.1
UCSC Genome Browser rAspTig1: GCA_023333525.1 rAspTig1: GCA_023333555.1

No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) rAspTig1 78.97 Gbp 47.20x 64.0 GiB
Dovetail Genomics rAspTig1 36.56 Gbp 21.85x 17.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.67 Gbp.
Last upload on 4 December 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
rAspTig1 PacBio HiFi (.fq) 78.97 Gbp 47.20x 64.0 GiB
Dovetail Genomics 36.56 Gbp 21.85x 17.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.67 Gbp.
Last upload on 4 December 2024.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 24 February 2025
rAspTig1.pri.cur.20250224.fasta.gz (520.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 84.45 Mbp 1 296.62 Mbp
20 5 75.28 Mbp 2 211.56 Mbp
30 7 58.22 Mbp 2 211.56 Mbp
40 10 53.48 Mbp 3 179.77 Mbp
50 14 41.56 Mbp 5 115.49 Mbp
60 18 34.35 Mbp 6 111.64 Mbp
70 24 23.98 Mbp 8 90.85 Mbp
80 33 14.83 Mbp 10 75.28 Mbp
90 48 8.14 Mbp 14 25.67 Mbp
100 295 8.89 Kbp 185 12.36 Kbp
1.000x 295 1.67 Gbp 185 1.67 Gbp
NG based on genome size 1.67 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 24 February 2025
rAspTig1.alt.decontam.20250224.fasta.gz (415.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 95.29 Mbp 1 272.93 Mbp
20 4 67.31 Mbp 2 120.08 Mbp
30 6 62.93 Mbp 3 117.01 Mbp
40 8 57.16 Mbp 4 112.66 Mbp
50 11 35.33 Mbp 5 98.36 Mbp
60 16 26.30 Mbp 7 91.77 Mbp
70 23 19.15 Mbp 9 74.14 Mbp
80 32 12.91 Mbp 11 39.54 Mbp
90 45 9.30 Mbp 17 14.92 Mbp
100 120 14.12 Kbp 78 14.12 Kbp
1.000x 120 1.44 Gbp 78 1.44 Gbp
NG based on genome size 1.67 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_CCGP from 24 February 2025
rAspTig1.MT.20250224.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_genbank/rAspTig1.yaml (view)
species: Aspidoscelis tigris
specimen: rAspTig1
projects: 
  - vgp
  - ccgp
assembled_by_group: California Conservation Genomics Project (CCGP)
data_location: S3
release_to: S3
hap1: s3://genomeark/species/Aspidoscelis_tigris/rAspTig1/assembly_genbank/rAspTig1.hap1.GCA_023333555.1.fasta.gz
hap2: s3://genomeark/species/Aspidoscelis_tigris/rAspTig1/assembly_genbank/rAspTig1.hap2.GCA_023333525.1.fasta.gz
pretext_hap1: s3://genomeark/species/Aspidoscelis_tigris/rAspTig1/assembly_genbank/evaluation/hap1/pretext/rAspTig1_hap1__s2.pretext
pretext_hap2: s3://genomeark/species/Aspidoscelis_tigris/rAspTig1/assembly_genbank/evaluation/hap2/pretext/rAspTig1_hap2__s2.pretext
kmer_spectra_img: s3://genomeark/species/Aspidoscelis_tigris/rAspTig1/assembly_genbank/evaluation/merqury/rAspTig1_png/
pacbio_read_dir: s3://genomeark/species/Aspidoscelis_tigris/rAspTig1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Aspidoscelis_tigris/rAspTig1/genomic_data/dovetail/
pipeline: 
  - hifiasm (0.16.1-r375)
  - purge-dups (1.2.6)
  - SALSA (2)
notes: This was a Hifiasm-HiC assembly of rAspTig1, assembled by the CCGP and present on NCBI as GCA_023333555.1 (hap1) and GCA_023333525.1 (hap2). The haplotypes were labeled on GenBank as "principal" and "alternate", respectively. However, we are labeling the "alternate" as hap1 because it is the more complete, higher quality assembly. Dovetail Omni-C for the HiC. This is a VGP Phase 1 species we are submitting for curation.
Data Use Policy

Samples and data come from a variety of sources. To support fair and productive use of this data, please abide by the Data Use Policy and contact Erich D. Jarvis, ejarvis@rockefeller.edu, with any questions.