Myiarchus magnirostris

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) bMyiMag1 99.13 Gbp N/A 45.7 GiB
PacBio HiFi (.bam) bMyiMag1 101.76 Gbp N/A 337.4 GiB
Arima bMyiMag1 72.70 Gbp N/A 39.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 12 March 2026.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bMyiMag1 PacBio HiFi (.fq) 99.13 Gbp N/A 45.7 GiB
PacBio HiFi (.bam) 101.76 Gbp N/A 337.4 GiB
Arima 72.70 Gbp N/A 39.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 12 March 2026.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 6 April 2026
bMyiMag1.HiC.hap1.20260406.fasta.gz (277.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 1 114.72 Mbp 1 233.70 Mbp
20 3 65.74 Mbp 1 233.70 Mbp
30 5 47.63 Mbp 2 97.23 Mbp
40 7 44.04 Mbp 4 74.48 Mbp
50 10 26.42 Mbp 5 65.04 Mbp
60 14 21.30 Mbp 7 46.78 Mbp
70 20 17.54 Mbp 10 25.77 Mbp
80 26 12.61 Mbp 14 21.26 Mbp
90 38 6.69 Mbp 20 14.61 Mbp
100 300 17.59 Kbp 163 17.59 Kbp
1.000x 300 1.04 Gbp 163 1.04 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 6 April 2026
bMyiMag1.HiC.hap2.20260406.fasta.gz (295.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 1 114.76 Mbp 1 117.68 Mbp
20 3 74.23 Mbp 2 116.16 Mbp
30 5 44.11 Mbp 4 75.39 Mbp
40 7 36.68 Mbp 5 74.23 Mbp
50 11 24.59 Mbp 7 65.23 Mbp
60 16 20.45 Mbp 8 56.43 Mbp
70 23 15.00 Mbp 11 31.22 Mbp
80 31 11.14 Mbp 16 20.89 Mbp
90 46 5.06 Mbp 22 14.68 Mbp
100 280 17.19 Kbp 128 17.19 Kbp
1.000x 280 1.11 Gbp 128 1.11 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 15 April 2026
bMyiMag1.MT.20260415.fasta.gz (0.8 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/bMyiMag1.yml (view)
species: Myiarchus magnirostris
specimem: bMyiMag1
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Myiarchus_magnirostris/bMyiMag1/assembly_vgp_HiC_2.0/bMyiMag1.HiC.hap1.20260406.fasta.gz
hap2: s3://genomeark/species/Myiarchus_magnirostris/bMyiMag1/assembly_vgp_HiC_2.0/bMyiMag1.HiC.hap2.20260406.fasta.gz
pretext_hap1: s3://genomeark/species/Myiarchus_magnirostris/bMyiMag1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/bMyiMag1_hap1_s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Myiarchus_magnirostris/bMyiMag1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/bMyiMag1_hap2_s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Myiarchus_magnirostris/bMyiMag1/assembly_vgp_HiC_2.0/evaluation/merqury/bMyiMag1_png/
pacbio_read_dir: s3://genomeark/species/Myiarchus_magnirostris/bMyiMag1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Myiarchus_magnirostris/bMyiMag1/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy3)
  - yahs (1.2a.2+galaxy3)
  - VGP1 genomic profiling workflow (v20260331)
  - VGP4 HiFi HiC assembly workflow (v0.6)
  - VGP8 HiC scaffolding workflow (v3.5) with mapq=10
  - VGP9 decontamination workflow (v1.3) 
  - Pre-curation worklfow (v20260330) with mapq=10, remove HiC duplicates and generate high-resolution map
notes: This was a Hifiasm-HiC assembly of bMyiMag1 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 mitogenome is assembled manually. There are lots of NUMT reads in the raw HiFi reads (see QC report on GenomeArk). Three reads appeared to have fewer variants and limited soft-clipping after inspecting the HiFi reads alignment against the another bird species Tyrannus savana mitogenome (accesssion NC_051025.1). 
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.