Melanerpes carolinus

- S3 File Index -- S3 Interactive Viewer -- NCBI Taxonomy Browser -


No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bMelCao1 86.93 Gbp N/A 41.4 GiB
PacBio HiFi (.bam) bMelCao1 89.18 Gbp N/A 291.7 GiB
Arima bMelCao1 228.90 Gbp N/A 122.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 31 October 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bMelCao1 PacBio HiFi (.fq) 86.93 Gbp N/A 41.4 GiB
PacBio HiFi (.bam) 89.18 Gbp N/A 291.7 GiB
Arima 228.90 Gbp N/A 122.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 31 October 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 24 November 2025
bMelCao1.HiC.hap1.20251124.fasta.gz (345.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 8 16.33 Mbp 2 94.88 Mbp
20 18 11.56 Mbp 3 85.73 Mbp
30 32 8.38 Mbp 5 64.35 Mbp
40 53 6.19 Mbp 8 55.71 Mbp
50 79 4.87 Mbp 10 45.95 Mbp
60 114 3.63 Mbp 14 28.72 Mbp
70 165 2.28 Mbp 20 21.57 Mbp
80 255 1.14 Mbp 28 16.94 Mbp
90 446 496.66 Kbp 48 1.96 Mbp
100 1535 7.39 Kbp 776 7.39 Kbp
1.000x 1535 1.47 Gbp 776 1.47 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 24 November 2025
bMelCao1.HiC.hap2.20251124.fasta.gz (333.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 6 20.40 Mbp 1 136.76 Mbp
20 14 12.92 Mbp 3 81.61 Mbp
30 26 10.14 Mbp 5 63.63 Mbp
40 41 7.18 Mbp 7 58.30 Mbp
50 63 5.10 Mbp 9 52.77 Mbp
60 92 3.94 Mbp 12 36.64 Mbp
70 135 2.60 Mbp 17 26.17 Mbp
80 199 1.65 Mbp 22 20.07 Mbp
90 328 0.66 Mbp 30 13.63 Mbp
100 1022 17.26 Kbp 345 17.26 Kbp
1.000x 1022 1.34 Gbp 345 1.34 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 24 November 2025
bMelCao1.MT.20251124.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bMelCao1.yml (view)
species: Melanerpes carolinus
specimem: bMelCao1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Melanerpes_carolinus/bMelCao1/assembly_vgp_HiC_2.0/bMelCao1.HiC.hap1.20251124.fasta.gz
hap2: s3://genomeark/species/Melanerpes_carolinus/bMelCao1/assembly_vgp_HiC_2.0/bMelCao1.HiC.hap2.20251124.fasta.gz
pretext_hap1: s3://genomeark/species/Melanerpes_carolinus/bMelCao1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/bMelCao1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Melanerpes_carolinus/bMelCao1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/bMelCao1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Melanerpes_carolinus/bMelCao1/assembly_vgp_HiC_2.0/evaluation/merqury/bMelCao1_png/
pacbio_read_dir: s3://genomeark/species/Melanerpes_carolinus/bMelCao1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Melanerpes_carolinus/bMelCao1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy3)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v0.6)
  - VGP4 HiFi HiC assembly workflow (v0.4)
  - VGP8 HiC scaffolding workflow (v3.1) with mapq=10
  - VGP9 decontamination workflow (v1.2) 
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of bMelCao1 resulting in two haplotype assemblies. HiC data were generated using the Arima library prep kit, and require trimming the first 5 bp off from the 5' end of both read files. The restriction enzymes used were the Arima v2 kit, so the cutting sites are GATC, GANTC, CTNAG, TTAA.
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.