Hoplias malabaricus

trahira

Included in the VGP.

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


Resource Primary Assembly Alternate Assembly
GenBank fHopMal1: GCA_029633855.1 fHopMal1: GCA_029633875.1
ENA fHopMal1: GCA_029633855.1 fHopMal1: GCA_029633875.1
UCSC Genome Browser fHopMal1: GCA_029633855.1 fHopMal1: GCA_029633875.1

metadata.yaml (view) (edit on github)
species:
  name: Hoplias malabaricus
  individuals:
  - short_name: fHopMal1
  short_name: fHopMal
  taxon_id: 27720
  common_name: trahira
  genome_size: 1252000000
  genome_size_method: GoAT
  order:
    name: Characiformes
  family:
    name: Erythrinidae
  project: [ vgp ]
CC BY-NC 2.0 Fernando Dagosta (flickr)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) fHopMal1 33.64 Gbp 26.87x 24.2 GiB
PacBio HiFi (.bam) fHopMal1 15.49 Gbp 12.37x 53.8 GiB
Arima fHopMal1 57.37 Gbp 45.82x 29.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.25 Gbp.
Last upload on 5 October 2022.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fHopMal1 PacBio HiFi (.fq) 33.64 Gbp 26.87x 24.2 GiB
PacBio HiFi (.bam) 15.49 Gbp 12.37x 53.8 GiB
Arima 57.37 Gbp 45.82x 29.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.25 Gbp.
Last upload on 5 October 2022.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 19 June 2023
fHopMal1.hap1.cur.20230619.fasta.gz (298.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 6 17.89 Mbp 2 90.65 Mbp
20 15 11.62 Mbp 3 86.20 Mbp
30 29 7.00 Mbp 5 73.28 Mbp
40 52 4.30 Mbp 7 57.28 Mbp
50 87 3.14 Mbp 9 47.62 Mbp
60 141 1.83 Mbp 12 44.50 Mbp
70 238 0.97 Mbp 15 41.56 Mbp
80 441 369.06 Kbp 18 38.39 Mbp
90 0 23 2.86 Mbp
100 0 0
0.893x 1575 1.12 Gbp 591 1.18 Gbp
NG based on genome size 1.25 Gbp.
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 19 June 2023
fHopMal1.hap2.cur.20230619.fasta.gz (260.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 7 15.07 Mbp 2 88.75 Mbp
20 18 9.04 Mbp 3 82.02 Mbp
30 34 6.50 Mbp 5 62.70 Mbp
40 58 4.50 Mbp 7 48.96 Mbp
50 94 2.48 Mbp 10 45.08 Mbp
60 168 1.29 Mbp 13 39.88 Mbp
70 337 439.90 Kbp 16 38.19 Mbp
80 0 126 111.54 Kbp
90 0 0
100 0 0
0.785x 1230 0.98 Gbp 443 1.02 Gbp
NG based on genome size 1.25 Gbp.
Assembly Metadata
assembly_vgp_HiC_2.0/fHopMal1.yaml (view)
species: Hoplias malabaricus
specimen: fHopMal1
projects: 
  - vgp
hap1: s3://genomeark/species/Hoplias_malabaricus/fHopMal1/assembly_vgp_HiC_2.0/fHopMal1.HiC.hap1.20221005.fasta.gz
hap2: s3://genomeark/species/Hoplias_malabaricus/fHopMal1/assembly_vgp_HiC_2.0/fHopMal1.HiC.hap2.20221005.fasta.gz
pretext_hap1: s3://genomeark/species/Hoplias_malabaricus/fHopMal1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/fHopMal1_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Hoplias_malabaricus/fHopMal1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/fHopMal1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Hoplias_malabaricus/fHopMal1/assembly_vgp_HiC_2.0/evaluation/merqury/fHopMal1_png/
pacbio_read_dir: s3://genomeark/species/Hoplias_malabaricus/fHopMal1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
bionano_cmap_dir: s3://genomeark/species/Hoplias_malabaricus/fHopMal1/genomic_data/bionano/
hic_read_dir: s3://genomeark/species/Hoplias_malabaricus/fHopMal1/genomic_data/arima/
hic_kit: Arima2
pipeline:
  - hifiasm (0.16.1+galaxy3)
  - solve (3.7)
  - yahs (1.2a.2+galaxy0)
assembled_by_group: Rockefeller
notes: This was a hifiasm-HiC assembly of fHopMal1, resulting in two complete haplotypes. This individual had bionano data. HiC scaffolding was performed with YAHS. The kmer spectra indicates a homogametic specimen. We are submitting hap2 for curation, though file locations for hap1 are included here in case it is useful. 
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.