Kantor, Rose · Shakya, Migun · Ruth, Nelson · et al.
hybrid · semantic + lexical · 3 datasets ranked · 0.64s
Kantor, Rose · Shakya, Migun · Ruth, Nelson · et al.
A virus genome database representing 21,015 near-complete virus genomes collected from untargeted ultra-deep RNA/DNA combined sequencing of wastewater. Sequence data was provided by the CASPER consortium and raw data may be found on NCBI SRA under bioprojects PRJNA1247874 and PRJNA1198001. Data underwent read trimming, rRNA and human read removal, de novo assembly, and selection of high-quality viral contigs. Contigs were clustered at 95% identity and 85% query coverage to dereplicate. Chimera-checking required at least two independent assemblies of the same viral genome or presence of the genome in another reference database. Annotation made use of RdRpCATCH, geNomad, checkV, BLASTN against NCBI core-nt, and RNAVirHost. The RdRp fasta files contain representative RdRp sequences identified through homology to major RdRp reference databases and clustered at 90% sequence identity over 75% sequence coverage. Included sequences contain all three conserved RdRp motifs (A, B, and C) arranged in either the canonical ABC configuration or the permuted CAB configuration.
Manghi, Paolo
2 files · 8.0 MB · gzip, tsv
Using gene-level and species-level shotgun metagenomics, we provide the first characterization of the rural, Bolivian microbiome; we identified microbial genes which strongly correlate (rho>0.45) with arsenic in urine, and that overall contribute to substantiate that the gut microbiome helps tolerate arsenic via a evict-out-of-house mechanism. Mediation analysis, followed by phylogenetic investigation of metagenomic-assembled genomes, further strengthens this observation. This study elucidates the role of the microbiome in helping to tolerate arsenic-rich environments, and paves the way for probiotic interventions that may mitigate the effects of this toxic metal. This repository contains 2,478 HQ MAGs from the MicroToxBol cohort in fasta format and a descriptive table comprising taxonomic annotation, quality-checks, and coverage estimation.
Bar, Ido
9 files · 8.0 MB · gff, gzip
These files are downsampled WGS fastq files (250k paired-end reads each) of a fungal pathogen ( Ascochyta rabiei ), generated on MGI DNSeq-T7. The files are intended to be used directly as test datasets in PopFun - a Nextflow pipeline for variant calling in fungal genomes.