Cryptobranchus alleganiensis

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) aCryAll3 878.36 Gbp N/A 560.8 GiB
PacBio HiFi (.bam) aCryAll3 3158.29 Gbp N/A 4.0 TiB
Arima aCryAll3 6602.53 Gbp N/A 3.1 TiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 3 November 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
aCryAll3 PacBio HiFi (.fq) 878.36 Gbp N/A 560.8 GiB
PacBio HiFi (.bam) 3158.29 Gbp N/A 4.0 TiB
Arima 6602.53 Gbp N/A 3.1 TiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 3 November 2025.
Assemblies
Individual 3 Haplotype 1 Assembly
Version assembly_curated from 13 July 2026
aCryAll3.hap1.cur.20260713.fasta.gz (12.4 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 128 26.99 Mbp 1 7.29 Gbp
20 358 17.25 Mbp 2 6.88 Gbp
30 698 12.16 Mbp 3 6.33 Gbp
40 1180 8.57 Mbp 3 6.33 Gbp
50 1849 6.20 Mbp 4 5.07 Gbp
60 2802 4.19 Mbp 6 2.47 Gbp
70 4281 2.64 Mbp 9 1.51 Gbp
80 6729 1.50 Mbp 13 0.88 Gbp
90 11572 0.66 Mbp 26 176.18 Mbp
100 39696 6.03 Kbp 15805 6.78 Kbp
1.000x 39696 48.79 Gbp 15805 48.79 Gbp
NG based on genome size .
Individual 3 Haplotype 2 Assembly
Version assembly_curated from 13 July 2026
aCryAll3.hap2.cur.20260713.fasta.gz (12.1 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 128 25.79 Mbp 1 7.22 Gbp
20 360 16.68 Mbp 2 6.62 Gbp
30 707 11.57 Mbp 3 6.18 Gbp
40 1202 8.13 Mbp 3 6.18 Gbp
50 1900 5.71 Mbp 4 5.00 Gbp
60 2892 3.99 Mbp 6 2.41 Gbp
70 4385 2.57 Mbp 8 1.75 Gbp
80 6795 1.49 Mbp 12 0.84 Gbp
90 11475 0.68 Mbp 27 152.69 Mbp
100 36507 8.51 Kbp 13453 8.60 Kbp
1.000x 36507 47.42 Gbp 13453 47.43 Gbp
NG based on genome size .
Individual 3 Mitochondrial Assembly
Version assembly_MT_rockefeller from 4 August 2025
aCryAll3.MT.20250804.fasta.gz (5.2 KiB)

Quality: not computed
Assembly Metadata
assembly_rockefeller/aCryAll3.yml (view)
species: Cryptobranchus alleganiensis
specimem: aCryAll3
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Cryptobranchus_alleganiensis/aCryAll3/assembly_rockefeller/aCryAll3.standard.hap1.20260420.fasta.gz
hap2: s3://genomeark/species/Cryptobranchus_alleganiensis/aCryAll3/assembly_rockefeller/aCryAll3.standard.hap2.20260420.fasta.gz
pretext_hap1: s3://genomeark/species/Cryptobranchus_alleganiensis/aCryAll3/assembly_rockefeller/evaluation/hap1/pretext/s2/aCryAll3_hap1_s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Cryptobranchus_alleganiensis/aCryAll3/assembly_rockefeller/evaluation/hap2/pretext/s2/aCryAll3_hap2_s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Cryptobranchus_alleganiensis/aCryAll3/assembly_rockefeller/evaluation/merqury/aCryAll3_png/
pacbio_read_dir: s3://genomeark/species/Cryptobranchus_alleganiensis/aCryAll3/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Cryptobranchus_alleganiensis/aCryAll3/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0-r726) `hifiasm -o hellbender_HiFi.asm -t 64 $DIR/genomic_data/pacbio_hifi/*.fastq.gz`
  - yahs (1.2.2) `yahs $HAP1 $DIR/hap1_merged_markdup_q10.bam -o hap1_yahs -e 'GATC,GANTC,CTNAG,TTAA' --no-contig-ec` `yahs $HAP2 $DIR/hap2_merged_markdup_q10.bam -o hap2_yahs -e 'GATC,GANTC,CTNAG,TTAA' --no-contig-ec`
  - gfastats (1.3.12)
  - bwa (0.7.19-r1273)
  - samtools (1.22)
  - bandage (0.9.0)
  - genomescope (2.1.0+galaxy0)
  - meryl (1.4.1)
  - merqury (1.3)
  - compleasm (0.2.6)
  - PretextMap (0.2.4)
  - PretextSnapshot (0.0.5)
  - teloscope (0.1.4)
  - minimap2 (2.30-r1287)
  - bamcoverage (3.5.6)
  - VGP0 mitoHiFi workflow (v0.2.1)
notes: This was a Hifiasm (HiFi only) assembly of aCryAll3 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.