Neotoma floridana

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mNeoFlo1 162.58 Gbp N/A 73.3 GiB
PacBio HiFi (.bam) mNeoFlo1 164.99 Gbp N/A 609.0 GiB
Arima mNeoFlo1 266.44 Gbp N/A 144.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 24 September 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mNeoFlo1 PacBio HiFi (.fq) 162.58 Gbp N/A 73.3 GiB
PacBio HiFi (.bam) 164.99 Gbp N/A 609.0 GiB
Arima 266.44 Gbp N/A 144.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 24 September 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 7 April 2025
mNeoFlo1.hap1.cur.20250407.fasta.gz (0.9 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 5 68.65 Mbp 2 170.14 Mbp
20 10 58.15 Mbp 4 161.29 Mbp
30 16 46.92 Mbp 6 146.25 Mbp
40 24 36.95 Mbp 9 115.32 Mbp
50 34 28.56 Mbp 12 95.01 Mbp
60 47 18.56 Mbp 16 84.36 Mbp
70 69 11.69 Mbp 20 72.86 Mbp
80 112 4.69 Mbp 25 46.13 Mbp
90 245 1.37 Mbp 116 1.52 Mbp
100 1535 2.36 Kbp 1381 2.36 Kbp
1.000x 1535 3.23 Gbp 1381 3.23 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 7 April 2025
mNeoFlo1.hap2.cur.20250407.fasta.gz (735.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 4 71.80 Mbp 2 170.44 Mbp
20 8 60.61 Mbp 4 157.06 Mbp
30 14 45.40 Mbp 6 140.55 Mbp
40 21 36.24 Mbp 8 114.77 Mbp
50 29 30.01 Mbp 11 94.22 Mbp
60 39 23.63 Mbp 14 87.38 Mbp
70 56 14.32 Mbp 17 78.33 Mbp
80 79 8.64 Mbp 21 65.46 Mbp
90 162 1.40 Mbp 45 2.01 Mbp
100 1096 3.30 Kbp 942 3.85 Kbp
1.000x 1096 2.82 Gbp 942 2.82 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 11 October 2024
mNeoFlo1.MT.20241011.fasta.gz (5.2 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mNeoFlo1.yml.yaml (view)
species: Neotoma floridana
specimen: mNeoFlo1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Neotoma_floridana/mNeoFlo1/assembly_vgp_HiC_2.0/evaluation/mNeoFlo1.HiC.hap1.20241011.fasta.gz
hap2: s3://genomeark/species/Neotoma_floridana/mNeoFlo1/assembly_vgp_HiC_2.0/evaluation/mNeoFlo1.HiC.hap2.20241011.fasta.gz
pretext_hap1: s3://genomeark/species/Neotoma_floridana/mNeoFlo1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/mNeoFlo1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Neotoma_floridana/mNeoFlo1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/mNeoFlo1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Neotoma_floridana/mNeoFlo1/assembly_vgp_HiC_2.0/evaluation/merqury/mNeoFlo1_png/
pacbio_read_dir: s3://genomeark/species/Neotoma_floridana/mNeoFlo1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Neotoma_floridana/mNeoFlo1/genomic_data/arima/
mito: s3://genomeark/species/Neotoma_floridana/mNeoFlo1/assembly_MT_rockefeller/mNeoFlo1.MT.20241011
pipeline: 
  - hifiasm (0.19.9+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of mNeoFlo1, resulting in two complete haplotypes. HiC scaffolding was performed with YaHS. The HiC prep kit used was Arima library prep. The HiC reads needed to have 5 bp trimmed from the 5' end due to adapter left over from the Arima library prep kit. This is a VGP Phase 1 species we are submitting for dual 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.