Lonchura striata

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bLonStr1 83.35 Gbp N/A 40.6 GiB
PacBio HiFi (.bam) bLonStr1 82.44 Gbp N/A 328.5 GiB
Arima bLonStr1 115.02 Gbp N/A 63.6 GiB
Illumina bLonStr2 69.56 Gbp N/A 32.0 GiB
bLonStr3 68.57 Gbp N/A 31.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 29 August 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bLonStr1 PacBio HiFi (.fq) 83.35 Gbp N/A 40.6 GiB
PacBio HiFi (.bam) 82.44 Gbp N/A 328.5 GiB
Arima 115.02 Gbp N/A 63.6 GiB
bLonStr2 Illumina 69.56 Gbp N/A 32.0 GiB
bLonStr3 Illumina 68.57 Gbp N/A 31.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 29 August 2024.
Assemblies
Individual 1 Maternal Assembly
Version assembly_curated from 1 November 2024
bLonStr1.mat.cur.20241101.fasta.gz (327.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 90.33 Mbp 1 157.32 Mbp
20 3 69.51 Mbp 2 117.57 Mbp
30 5 58.32 Mbp 3 113.99 Mbp
40 8 35.64 Mbp 5 76.98 Mbp
50 11 29.14 Mbp 6 73.42 Mbp
60 16 20.99 Mbp 8 40.41 Mbp
70 24 8.65 Mbp 12 24.80 Mbp
80 43 4.51 Mbp 17 17.87 Mbp
90 80 2.13 Mbp 27 9.65 Mbp
100 337 15.12 Kbp 161 29.34 Kbp
1.000x 337 1.21 Gbp 161 1.21 Gbp
NG based on genome size .
Individual 1 Paternal Assembly
Version assembly_curated from 1 November 2024
bLonStr1.pat.cur.20241101.fasta.gz (323.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 77.46 Mbp 1 157.07 Mbp
20 4 74.05 Mbp 2 114.73 Mbp
30 5 61.36 Mbp 3 111.32 Mbp
40 7 47.65 Mbp 5 73.62 Mbp
50 11 31.06 Mbp 6 72.61 Mbp
60 17 17.85 Mbp 8 39.43 Mbp
70 25 9.19 Mbp 12 24.94 Mbp
80 44 3.79 Mbp 17 17.03 Mbp
90 94 1.46 Mbp 28 7.02 Mbp
100 430 9.13 Kbp 202 17.27 Kbp
1.000x 430 1.20 Gbp 202 1.20 Gbp
NG based on genome size .
Assembly Metadata
assembly_vgp_trio_2.0/bLonStr1.yml (view)
species: Lonchura striata
specimen: bLonStr1
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
mat: s3://genomeark/species/Lonchura_striata/bLonStr1/assembly_vgp_trio_2.0/bLonStr1.trio.mat.20240903.fasta.gz
pat: s3://genomeark/species/Lonchura_striata/bLonStr1/assembly_vgp_trio_2.0/bLonStr1.trio.pat.20240903.fasta.gz
pretext_mat: s3://genomeark/species/Lonchura_striata/bLonStr1/assembly_vgp_trio_2.0/evaluation/mat/pretext/bLonStr1_mat_s2.pretext
pretext_pat: s3://genomeark/species/Lonchura_striata/bLonStr1/assembly_vgp_trio_2.0/evaluation/pat/pretext/bLonStr1_pat_s2.pretext
kmer_spectra_img: s3://genomeark/species/Lonchura_striata/bLonStr1/assembly_vgp_trio_2.0/evaluation/merqury/bLonStr1_png/
pacbio_read_dir: s3://genomeark/species/Lonchura_striata/bLonStr1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Lonchura_striata/bLonStr1/genomic_data/arima/
pipeline: 
  - hifiasm (0.19.9+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a trio assembly of bLonStr1, resulting in two phased haplotypes. The father is bLonStr3 (hap1/pat) and the mother is bLonStr2 (hap2/mat). The assemblies underwent HiC (Arima) scaffolding. The HiC library prep kit was Arima, so 5bp need to be trimmed before use.
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.