Data · dataset · 2025
Cricetus cricetus bioinformatic data processing
Listed in Debreceni Egyetem Adattár
This is the bioinformatic pipeline we run to produce filtered vcf files for downstream analyses from raw reads.
Description
The steps include: (1.) demultiplexing, (2.) quality and sequence filtering, (3.) mapping to the reference, (4.) variant calling, (5.) basic filtering of vcf (imiss, meanDP, maf, biallelic, lmiss), (6.) LD pruning and keeping only SNPs. The vcf produced after step (5.) is suitable for phylogenetic tree reconstruction, the vcf produced after the last step is suitable for population genomics.
Links
Where it is published
- Dataverse dataset page adattar.unideb.hu/dataset.xhtml?persistentId=doi%3A10.48428%2FADATTAR%2FT3OMKJ ↗
landing page · from adattar unideb hu
- DOI doi.org/10.48428/adattar/t3omkj ↗
DOI / persistent id · from adattar unideb hu
Catalogue records · 1
- Dataverse API adattar.unideb.hu/api/datasets/:persistentId/?persistentId=doi%3A10.48428%2FADAT… ↗
metadata API · from adattar unideb hu
Topics
- Stated by source
- Computer and Information Science · Medicine, Health and Life Sciences
- From keywords
- Engineering · Humanities · Life Sciences · Medicine & Health · Social Science
Provenance · 1 source records, 13 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| Debreceni Egyetem Adattár | doi:10.48428/ADATTAR/T3OMKJ | 6 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| concepts[field].dataverse_subject:computer-and-information-science | source · adattar unideb hu | connector:adattar_unideb_hu@1.0.0 | /subjects |
| concepts[field].dataverse_subject:medicine-health-and-life-sciences | source · adattar unideb hu | connector:adattar_unideb_hu@1.0.0 | /subjects |
| concepts[field].local:field:engineering | mapping · adattar unideb hu | connector:adattar_unideb_hu@1.0.0 | /subjects |
| concepts[field].local:field:humanities | mapping · adattar unideb hu | connector:adattar_unideb_hu@1.0.0 | /subjects |
| concepts[field].local:field:life-sciences | mapping · adattar unideb hu | connector:adattar_unideb_hu@1.0.0 | /subjects |
| concepts[field].local:field:medicine-health | mapping · adattar unideb hu | connector:adattar_unideb_hu@1.0.0 | /subjects |
| concepts[field].local:field:social-science | mapping · adattar unideb hu | connector:adattar_unideb_hu@1.0.0 | /subjects |
| created_date | source · adattar unideb hu | connector:adattar_unideb_hu@1.0.0 | |
| description | source · adattar unideb hu | connector:adattar_unideb_hu@1.0.0 | /description |
| publication_date | source · adattar unideb hu | connector:adattar_unideb_hu@1.0.0 | |
| title | source · adattar unideb hu | connector:adattar_unideb_hu@1.0.0 | /name |
| updated_date | source · adattar unideb hu | connector:adattar_unideb_hu@1.0.0 | |
| version_label | source · adattar unideb hu | connector:adattar_unideb_hu@1.0.0 |