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 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.