Powered by OpenAIRE graph
Found an issue? Give us feedback
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
ZENODO
Dataset . 2024
License: CC BY
Data sources: ZENODO
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
ZENODO
Dataset . 2024
License: CC BY
Data sources: ZENODO
ZENODO
Dataset . 2024
License: CC BY
Data sources: Datacite
ZENODO
Dataset . 2024
License: CC BY
Data sources: Datacite
ZENODO
Dataset . 2024
License: CC BY
Data sources: Datacite
versions View all 3 versions
addClaim

Dataset supporting the tool 'delfies: a Python package for the detection of DNA breakpoints with neo-telomere addition'

Authors: Letcher, Brice;

Dataset supporting the tool 'delfies: a Python package for the detection of DNA breakpoints with neo-telomere addition'

Abstract

Purpose These data can be used to test my tool delfies on real data, to get a concrete sense of its inputs/outputs and test that it is properly installed. Description Genome I downloaded the genome of Oscheius onirici, accession: GCA_932521025. I subsampled the genome to the last 2kbp of chromosome I, which contains an elimination breakpoint, using `seqkit` v2.8.2, giving the FASTA file in this release. Sequencing data I then downloaded the following sequencing data for *O. onirici*, from the European Nucleotide Archive: ERR5967937: Illumina NovaSeq 6000 paired end short reads. Reads are 2x150bp with average per-base quality of Q27. ERR10796202: Oxford Nanopore PromethION long reads. Reads have average length 11.9kbp and average per-base quality Q11.4. ERR7979900: Pacific Biosciences (PacBio) Sequel II long reads. Reads have average length 11.1kbp and average per-base quality Q28. And aligned them to the above genome with `minimap2` version 2.26-r1175, using the following presets: "map-ont" for the Nanopore data, "map-hifi" for the PacBio data, "sr" for the Illumina data. After sorting with `samtools`, this gives the BAM files in this release. Running delfies I then ran `delfies` version 0.6.0 on each BAM and genome, as: ```shdelfies --threads 16 \ --telo_forward_seq TTAGGC \ --breakpoint_type all \ --min_mapq 20 \ --min_supporting_reads 6 \ \${genome} \${bam} \${odirname}``` The three resulting output directories are in this release, prefixed with `delfies_`. A single, identical breakpoint is found using all three BAMs (see files '*breakpoint_locations.bed'). Data source The above raw data were produced and released by the Wellcome Sanger Institute as part of projects PRJEB51305 and PRJEB59023.

Keywords

FOS: Computer and information sciences, Bioinformatics, Genomics

  • BIP!
    Impact byBIP!
    selected citations
    These citations are derived from selected sources.
    This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    1
    popularity
    This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
    Average
    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    Average
    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
    Average
Powered by OpenAIRE graph
Found an issue? Give us feedback
selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
1
Average
Average
Average