Carlito syrichta

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mCarSyr1 273.87 Gbp N/A 116.6 GiB
PacBio HiFi (.bam) mCarSyr1 280.25 Gbp N/A 0.9 TiB
Arima mCarSyr1 343.46 Gbp N/A 188.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 14 April 2026.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mCarSyr1 PacBio HiFi (.fq) 273.87 Gbp N/A 116.6 GiB
PacBio HiFi (.bam) 280.25 Gbp N/A 0.9 TiB
Arima 343.46 Gbp N/A 188.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 14 April 2026.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 15 June 2026
mCarSyr1.hap1.cur.20260615.fasta.gz (1.2 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 10 32.70 Mbp 3 124.03 Mbp
20 26 23.32 Mbp 7 100.93 Mbp
30 48 17.19 Mbp 11 96.86 Mbp
40 76 13.49 Mbp 16 91.55 Mbp
50 112 10.40 Mbp 21 86.71 Mbp
60 162 7.37 Mbp 26 84.18 Mbp
70 232 5.04 Mbp 32 71.61 Mbp
80 350 2.75 Mbp 38 61.15 Mbp
90 585 1.21 Mbp 70 3.95 Mbp
100 2063 3.92 Kbp 1114 3.92 Kbp
1.000x 2063 4.31 Gbp 1114 4.31 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 15 June 2026
mCarSyr1.hap2.cur.20260615.fasta.gz (0.9 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 9 32.88 Mbp 3 120.66 Mbp
20 24 23.20 Mbp 7 98.89 Mbp
30 43 16.04 Mbp 10 94.98 Mbp
40 68 13.26 Mbp 14 91.52 Mbp
50 99 10.40 Mbp 18 89.52 Mbp
60 139 8.06 Mbp 23 84.87 Mbp
70 195 5.28 Mbp 27 73.78 Mbp
80 284 3.06 Mbp 33 67.92 Mbp
90 463 1.29 Mbp 39 46.70 Mbp
100 1748 453 bp 777 4.50 Kbp
1.000x 1748 3.67 Gbp 777 3.67 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 20 May 2026
mCarSyr1.MT.20260520.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mCarSyr1.yml (view)
species: Carlito syrichta
specimen: mCarSyr1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Carlito_syrichta/mCarSyr1/assembly_vgp_HiC_2.0/mCarSyr1.HiC.hap1.20260520.fasta.gz
hap2: s3://genomeark/species/Carlito_syrichta/mCarSyr1/assembly_vgp_HiC_2.0/mCarSyr1.HiC.hap2.20260520.fasta.gz
pretext_hap1: s3://genomeark/species/Carlito_syrichta/mCarSyr1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/mCarSyr1_hap1_s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Carlito_syrichta/mCarSyr1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/mCarSyr1_hap2_s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Carlito_syrichta/mCarSyr1/assembly_vgp_HiC_2.0/evaluation/merqury/mCarSyr1_png/
pacbio_read_dir: s3://genomeark/species/Carlito_syrichta/mCarSyr1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Carlito_syrichta/mCarSyr1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy3)
  - yahs (1.2a.2+galaxy3)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v20260331)
  - VGP4 HiFi HiC assembly workflow (v0.6)
  - VGP8 HiC scaffolding workflow (v3.5) with mapq=10
  - VGP9 decontamination workflow (v1.3)
  - Pre-curation workflow (v2.4) with mapq=10, keep HiC duplicates and generate high-resolution map
notes: This was a Hifiasm-HiC assembly of mCarSyr1 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.