Custom FastQ Screen Database Panel for EpiTaxMAG (Water Surveillance)
Authors/Creators
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1.
Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana
Description
This dataset contains the compiled custom FastQ Screen database panel designed for the EpiTaxMAG pipeline (available at https://github.com/alesanzdro/epitaxmag). It was specifically built for environmental water surveillance to perform initial read screening, contamination detection, and baseline community profiling in metagenomics projects using Oxford Nanopore long reads.
The configuration is optimized for the minimap2 aligner using the map-ont preset. To facilitate rapid screening during the quality control step, the panel is categorized into logical biological groups: host DNA, sequencing controls, vectors, classic enteric pathogens, environmental opportunists, priority antimicrobial resistance (AMR) reservoirs, tropical zoonoses, source tracking markers, enteric viruses, and parasites.
File Information & Integrity
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Filename:
epitaxmag-fqs-panel-v1.tar.gz -
MD5:
5b963ab49cc2991c646e57e5f410f1ce -
SHA256:
243f4025351b6ddd572e2fe5d6fe81d477612fe7c8485976bf73d6e3abaf63c3
Database Contents Summary
Below is a detailed summary of the sequences contained within the compiled FASTA files:
| FASTA File | No. Sequences | Description of Content |
Vectors.fasta |
3,155 | Various sequencing adapters (Illumina, Nanopore, DNBSEQ), primers, and artificial cloning vectors. |
H_sapiens.fasta |
705 | Homo sapiens genome (chromosomes, alternate loci, unlocalized scaffolds, and genomic patches). |
Avian_Marker.fasta |
229 | Avian metagenome-assembled genomes (MAGs) and uncharacterized genomic scaffolds. |
N_fowleri.fasta |
83 | Naegleria fowleri mitochondrial genome and multiple chromosomal scaffolds (whole genome shotgun sequence). |
B_pseudomallei.fasta |
78 | Burkholderia pseudomallei whole genome shotgun sequence scaffolds. |
Parasites.fasta |
43 | Cryptosporidium parvum and Giardia intestinalis chromosomal scaffolds. |
Dorea.fasta |
36 | Dorea longicatena whole genome shotgun sequence scaffolds. |
B_ovatus.fasta |
19 | Bacteroides ovatus whole genome shotgun sequence scaffolds. |
Klebsiella.fasta |
7 | Klebsiella pneumoniae chromosome and multiple plasmids (pKPHS1-6). |
A_bouvetii.fasta |
6 | Acinetobacter bouvetii whole genome shotgun sequence scaffolds. |
E_faecalis.fasta |
4 | Enterococcus faecalis V583 chromosome and plasmids (pTEF1, pTEF2, pTEF3). |
E_faecium.fasta |
4 | Enterococcus faecium Aus0004 chromosome and plasmids (p1, p2, p3). |
Vibrio_spp.fasta |
4 | Vibrio cholerae and Vibrio parahaemolyticus complete chromosomes. |
A_baumannii.fasta |
3 | Acinetobacter baumannii ATCC 17978 chromosome and plasmids (pAB1, pAB2). |
Salmonella.fasta |
3 | Salmonella enterica serovars Typhimurium (chromosome/plasmid) and Typhi. |
Shigella.fasta |
3 | Shigella flexneri and Shigella dysenteriae (chromosome and plasmid). |
Virus_Enteric.fasta |
3 | Hepatitis A virus, Rotavirus A, and Passiflora latent carlavirus complete genomes. |
Aliarcobacter.fasta |
2 | Aliarcobacter cryaerophilus chromosome and plasmid pACRY43158. |
Controls.fasta |
2 | Enterobacteria phage lambda and Escherichia phage phiX174 complete genomes. |
Leptospira.fasta |
2 | Leptospira interrogans complete chromosome and plasmid. |
Adenovirus.fasta |
1 | Human adenovirus C complete genome. |
Aeromonas.fasta |
1 | Aeromonas hydrophila complete sequence. |
Arcobacter_butzleri.fasta |
1 | Aliarcobacter butzleri RM4018 complete sequence. |
B_graminisolvens.fasta |
1 | Bacteroides graminisolvens MAG. |
Campylobacter.fasta |
1 | Campylobacter jejuni chromosome. |
Ecoli.fasta |
1 | Escherichia coli str. K-12 substr. MG1655 complete genome. |
Legionella.fasta |
1 | Legionella pneumophila str. Philadelphia 1 complete sequence. |
M_avium.fasta |
1 | Mycobacterium avium 104 complete sequence. |
P_aeruginosa.fasta |
1 | Pseudomonas aeruginosa PAO1 complete genome. |
Phocaeicola_dorei.fasta |
1 | Phocaeicola dorei complete chromosome. |
Files
Files
(1.1 GB)
| Name | Size | Download all |
|---|---|---|
|
md5:5b963ab49cc2991c646e57e5f410f1ce
|
1.1 GB | Download |
Additional details
Software
- Repository URL
- https://github.com/alesanzdro/epitaxmag
- Development Status
- Active