Melospiza melodia

song sparrow

Included in the VGP.

- S3 File Index -- S3 Interactive Viewer -- NCBI Taxonomy Browser -


Resource Primary Assembly Alternate Assembly
GenBank bMelMel1: GCA_022749695.1 bMelMel1: GCA_022749775.1
ENA bMelMel1: GCA_022749695.1 bMelMel1: GCA_022749775.1
UCSC Genome Browser bMelMel1: GCA_022749695.1 bMelMel1: GCA_022749775.1

metadata.yaml (view) (edit on github)
species:
  name: Melospiza melodia
  individuals:
  - short_name: bMelMel1
  short_name: bMelMel
  taxon_id: '44397'
  common_name: song sparrow
  genome_size: 1399000000
  genome_size_method: GoAT
  order:
    name: Passeriformes
  family:
    name: Passerellidae
  project: [ vgp ]
CC BY-SA 4.0 Simon Pierre Barrette (Wikimedia)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) bMelMel2 742.27 Gbp 530.57x 1.3 TiB
PacBio HiFi (.fq) bMelMel2 42.63 Gbp 30.47x 35.0 GiB
PacBio HiFi (.bam) bMelMel2 88.56 Gbp 63.30x 68.6 GiB
Arima bMelMel2 145.05 Gbp 103.68x 70.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.40 Gbp.
Last upload on 14 August 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bMelMel2 PacBio HiFi (subreads) 742.27 Gbp 530.57x 1.3 TiB
PacBio HiFi (.fq) 42.63 Gbp 30.47x 35.0 GiB
PacBio HiFi (.bam) 88.56 Gbp 63.30x 68.6 GiB
Arima 145.05 Gbp 103.68x 70.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.40 Gbp.
Last upload on 14 August 2024.
Assemblies
Individual 2 Primary Assembly
Version assembly_curated from 21 August 2023
bMelMel2.pri.cur.20230821.fasta.gz (407.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 52.57 Mbp 1 173.22 Mbp
20 6 40.83 Mbp 2 142.30 Mbp
30 9 34.69 Mbp 3 138.71 Mbp
40 14 28.20 Mbp 5 95.15 Mbp
50 19 23.12 Mbp 6 82.36 Mbp
60 26 19.15 Mbp 8 51.68 Mbp
70 37 9.66 Mbp 12 31.76 Mbp
80 55 6.27 Mbp 17 20.78 Mbp
90 81 4.26 Mbp 26 13.70 Mbp
100 130 1.89 Mbp 38 9.04 Mbp
1.104x 653 1.54 Gbp 415 1.55 Gbp
NG based on genome size 1.40 Gbp.
Individual 2 Alternate Assembly
Version assembly_curated from 21 August 2023
bMelMel2.alt.cur.20230821.fasta.gz (360.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 8 15.41 Mbp 8 15.41 Mbp
20 19 10.89 Mbp 19 10.89 Mbp
30 35 7.27 Mbp 35 7.27 Mbp
40 58 5.22 Mbp 58 5.22 Mbp
50 90 3.65 Mbp 90 3.65 Mbp
60 135 2.59 Mbp 135 2.59 Mbp
70 205 1.49 Mbp 205 1.49 Mbp
80 330 0.80 Mbp 330 0.80 Mbp
90 692 179.54 Kbp 692 179.54 Kbp
100 0 0
0.969x 2328 1.36 Gbp 2328 1.36 Gbp
NG based on genome size 1.40 Gbp.
Individual 2 Mitochondrial Assembly
Version assembly_MT_rockefeller from 7 March 2023
bMelMel2.MT.20230307.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_standard_2.0/bMelMel2.yml (view)
species: Melospiza melodia
specimen: bMelMel2
projects: 
  - vgp
data_location: S3
release_to: S3
primary: s3://genomeark/species/Melospiza_melodia/bMelMel2/assembly_vgp_standard_2.0/bMelMel2.standard.pri.20230308.fasta.gz
haplotigs: s3://genomeark/species/Melospiza_melodia/bMelMel2/assembly_vgp_standard_2.0/bMelMel2.standard.alt.20230308.fasta.gz
pretext: s3://genomeark/species/Melospiza_melodia/bMelMel2/assembly_vgp_standard_2.0/evaluation/pri/pretext/bMelMel2_pri__s2.heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Melospiza_melodia/bMelMel2/assembly_vgp_standard_2.0/evaluation/merqury/bMelMel2_png/
mito: s3://genomeark/species/Melospiza_melodia/bMelMel2/assembly_MT_rockefeller/bMelMel2.MT.20230307.fasta.gz
pacbio_read_dir: s3://genomeark/species/Melospiza_melodia/bMelMel2/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Melospiza_melodia/bMelMel2/genomic_data/arima/
bionano_cmap_dir: s3://genomeark/species/Melospiza_melodia/bMelMel2/genomic_data/bionano/
pipeline:
  - hifiasm (0.18.8+galaxy1)
  - solve (3.7)
  - yahs (1.2a.2+galaxy0)
assembled_by_group: Rockefeller
notes: This was a primary/alternate assembly of bMelMel2 (VGL-bMelMel1). This individual had bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2. This sample arrived with metadata indicating it is a female. 
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.