Marmota flaviventris

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mMarFla1 151.25 Gbp N/A 74.1 GiB
PacBio HiFi (.bam) mMarFla1 150.65 Gbp N/A 599.3 GiB
Arima mMarFla1 192.81 Gbp N/A 104.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 8 March 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mMarFla1 PacBio HiFi (.fq) 151.25 Gbp N/A 74.1 GiB
PacBio HiFi (.bam) 150.65 Gbp N/A 599.3 GiB
Arima 192.81 Gbp N/A 104.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 8 March 2024.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 21 March 2024
mMarFla1.HiC.hap1.20240321.fasta.gz (778.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 108.34 Mbp 2 200.80 Mbp
20 5 97.75 Mbp 3 177.23 Mbp
30 9 78.08 Mbp 5 162.61 Mbp
40 13 62.65 Mbp 6 156.41 Mbp
50 18 46.97 Mbp 8 136.27 Mbp
60 24 34.61 Mbp 11 119.88 Mbp
70 33 26.06 Mbp 13 101.61 Mbp
80 46 14.64 Mbp 16 83.34 Mbp
90 89 2.47 Mbp 19 62.71 Mbp
100 1801 10.47 Kbp 1578 10.47 Kbp
1.000x 1801 2.71 Gbp 1578 2.71 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 21 March 2024
mMarFla1.HiC.hap2.20240321.fasta.gz (720.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 82.28 Mbp 2 199.88 Mbp
20 6 74.43 Mbp 3 175.05 Mbp
30 10 68.62 Mbp 4 166.43 Mbp
40 14 57.43 Mbp 6 157.46 Mbp
50 18 47.54 Mbp 8 136.55 Mbp
60 25 34.16 Mbp 10 120.12 Mbp
70 33 27.46 Mbp 12 104.43 Mbp
80 44 18.03 Mbp 14 89.64 Mbp
90 70 4.61 Mbp 18 60.29 Mbp
100 768 14.38 Kbp 542 14.38 Kbp
1.000x 768 2.49 Gbp 542 2.49 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 13 May 2024
mMarFla1.MT.20240513.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mMarFla1.yml (view)
species: Marmota flaviventris
specimen: mMarFla1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Marmota_flaviventris/mMarFla1/assembly_vgp_HiC_2.0/mMarFla1.HiC.hap1.20240321.fasta.gz
hap2: s3://genomeark/species/Marmota_flaviventris/mMarFla1/assembly_vgp_HiC_2.0/mMarFla1.HiC.hap2.20240321.fasta.gz
pretext_hap1: s3://genomeark/species/Marmota_flaviventris/mMarFla1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/mMarFla1_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Marmota_flaviventris/mMarFla1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/mMarFla1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Marmota_flaviventris/mMarFla1/assembly_vgp_HiC_2.0/evaluation/merqury/mMarFla1_png/
pacbio_read_dir: s3://genomeark/species/Marmota_flaviventris/mMarFla1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Marmota_flaviventris/mMarFla1/genomic_data/arima/
mito: s3://genomeark/species/Marmota_flaviventris/mMarFla1/assembly_MT_rockefeller/mMarFla1.MT.20240513.fasta.gz
pipeline: 
  - hifiasm (0.19.8+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of mMarFla1, 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. 
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.