Myotis sodalis

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mMyoSod1 146.73 Gbp N/A 74.3 GiB
PacBio HiFi (.bam) mMyoSod1 152.16 Gbp N/A 507.0 GiB
Arima mMyoSod1 128.30 Gbp N/A 71.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 November 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mMyoSod1 PacBio HiFi (.fq) 146.73 Gbp N/A 74.3 GiB
PacBio HiFi (.bam) 152.16 Gbp N/A 507.0 GiB
Arima 128.30 Gbp N/A 71.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 November 2025.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 27 January 2026
mMyoSod1.HiC.hap1.20260127.fasta.gz (547.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 154.36 Mbp 1 453.30 Mbp
20 3 123.70 Mbp 1 453.30 Mbp
30 5 84.29 Mbp 2 216.98 Mbp
40 8 72.15 Mbp 4 122.64 Mbp
50 11 65.07 Mbp 6 108.64 Mbp
60 14 54.05 Mbp 8 94.78 Mbp
70 18 49.11 Mbp 10 84.29 Mbp
80 23 38.74 Mbp 13 62.67 Mbp
90 31 17.56 Mbp 16 55.52 Mbp
100 223 21.21 Kbp 167 21.21 Kbp
1.000x 223 2.10 Gbp 167 2.10 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 27 January 2026
mMyoSod1.HiC.hap2.20260127.fasta.gz (516.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 157.19 Mbp 1 289.28 Mbp
20 3 136.87 Mbp 2 239.56 Mbp
30 5 100.79 Mbp 3 217.22 Mbp
40 7 95.14 Mbp 4 109.54 Mbp
50 9 62.89 Mbp 6 95.36 Mbp
60 13 54.54 Mbp 8 85.85 Mbp
70 16 49.07 Mbp 10 79.74 Mbp
80 21 32.51 Mbp 13 60.07 Mbp
90 29 17.17 Mbp 17 47.60 Mbp
100 165 25.11 Kbp 115 25.11 Kbp
1.000x 165 1.98 Gbp 115 1.98 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 27 January 2026
mMyoSod1.MT.20260127.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mMyoSod1.yml (view)
species: Myotis sodalis
specimem: mMyoSod1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Myotis_sodalis/mMyoSod1/assembly_vgp_HiC_2.0/mMyoSod1.HiC.hap1.20260127.fasta.gz
hap2: s3://genomeark/species/Myotis_sodalis/mMyoSod1/assembly_vgp_HiC_2.0/mMyoSod1.HiC.hap2.20260127.fasta.gz
pretext_hap1: s3://genomeark/species/Myotis_sodalis/mMyoSod1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/mMyoSod1_hap1_s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Myotis_sodalis/mMyoSod1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/mMyoSod1_hap2_s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Myotis_sodalis/mMyoSod1/assembly_vgp_HiC_2.0/evaluation/merqury/mMyoSod1_png/
pacbio_read_dir: s3://genomeark/species/Myotis_sodalis/mMyoSod1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Myotis_sodalis/mMyoSod1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy3)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v0.6)
  - VGP4 HiFi HiC assembly workflow (v0.4)
  - VGP8 HiC scaffolding workflow (v3.2) with mapq=10
  - VGP9 decontamination workflow (v1.2) 
  - VGP6 purge-dup workflow (v0.10.4)
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of mMyoSod1 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. The mitoHiFi assembly is twice the expected length and contains 59 annotated genes. Self-alignment of the mito-assembly in NCBI suggests that two mitogenomes were assembled into a single contig. Therefore, the assembly was trimmed to retain only the first half and re-annotated using MITOS2 (2.1.10+galaxy0) on galaxy.
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.