Latimeria chalumnae

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) fLatCha1 123.61 Gbp 41.94x 59.1 GiB
PacBio HiFi (.bam) fLatCha1 1043.32 Gbp 353.96x 498.7 GiB
Arima fLatCha2 242.39 Gbp 82.23x 128.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.95 Gbp.
Last upload on 19 March 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fLatCha1 PacBio HiFi (.fq) 123.61 Gbp 41.94x 59.1 GiB
PacBio HiFi (.bam) 1043.32 Gbp 353.96x 498.7 GiB
fLatCha2 Arima 242.39 Gbp 82.23x 128.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.95 Gbp.
Last upload on 19 March 2024.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 22 February 2024
fLatCha1.pri.cur.20240222.fasta.gz (774.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 93.00 Mbp 1 432.07 Mbp
20 6 77.49 Mbp 2 383.79 Mbp
30 11 57.81 Mbp 3 287.41 Mbp
40 16 46.93 Mbp 4 264.12 Mbp
50 23 42.08 Mbp 5 188.11 Mbp
60 30 34.81 Mbp 7 160.16 Mbp
70 41 22.98 Mbp 9 103.74 Mbp
80 56 15.60 Mbp 13 50.99 Mbp
90 81 8.22 Mbp 20 34.27 Mbp
100 351 7.79 Kbp 197 7.79 Kbp
1.000x 351 2.95 Gbp 197 2.95 Gbp
NG based on genome size 2.95 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 9 January 2024
fLatCha1.alt.cur.20240109.fasta.gz (385.6 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 882 100.23 Kbp 882 100.23 Kbp
20 2552 68.90 Kbp 2552 68.90 Kbp
30 4769 55.12 Kbp 4769 55.12 Kbp
40 7467 46.13 Kbp 7467 46.13 Kbp
50 10647 39.70 Kbp 10647 39.70 Kbp
60 14236 36.07 Kbp 14236 36.07 Kbp
70 18151 33.19 Kbp 18151 33.19 Kbp
80 22431 30.04 Kbp 22431 30.04 Kbp
90 27313 25.03 Kbp 27313 25.03 Kbp
100 34012 80 bp 34011 8.43 Kbp
1.000x 34012 1.35 Gbp 34011 1.35 Gbp
NG based on genome size 2.95 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 15 December 2023
fLatCha1.MT.20231215.fasta.gz (5.2 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_standard_2.0/fLatCha1.yml (view)
species: Latimeria chalumnae
specimen: fLatCha1
projects: 
  - vgp
data_location: S3
release_to: S3
primary: s3://genomeark/species/Latimeria_chalumnae/fLatCha1/assembly_vgp_standard_2.0/fLatCha1.standard.pri.20231215.fasta.gz
haplotigs: s3://genomeark/species/Latimeria_chalumnae/fLatCha1/assembly_vgp_standard_2.0/fLatCha1.standard.alt.20231215.fasta.gz
pretext: s3://genomeark/species/Latimeria_chalumnae/fLatCha1/assembly_vgp_standard_2.0/evaluation/pri/pretext/fLatCha1_pri__s2.heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Latimeria_chalumnae/fLatCha1/assembly_vgp_standard_2.0/evaluation/merqury_purgedalt/fLatCha1_png/
mito: s3://genomeark/species/Latimeria_chalumnae/fLatCha1/assembly_MT_rockefeller/fLatCha1.MT.20231215.fasta.gz
pacbio_read_dir: s3://genomeark/species/Latimeria_chalumnae/fLatCha1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Latimeria_chalumnae/fLatCha1/genomic_data/arima/
pipeline:
  - hifiasm (0.18.8+galaxy1)
  - yahs (1.2a.2+galaxy1)
assembled_by_group: Rockefeller
notes: This was a primary/alternate assembly of fLatCha1. This is a VGP Phase 1 species. This individual did not have bionano data. HiC scaffolding was performed with yahs. The HiC prep was Arima kit 2. The HiC library kit was Arima. The HiC data came from a different individual, fLatCha2.  Purge_dups was used on the alternate assembly, but not on the primary assembly. The only purging on the primary assembly was Hifiasm's default purging when running in pseudohaplotype mode. 
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.