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12 results for “snakemake”
Snakemake workflow for bacterial assembly QC update v1.0.1
<p>This repository contains a Snakemake bacterial assembly QC workflow to perform quality control on assembly files. It will use Quast (metrics), CheckM2 (completedness and contamination), Busco (completedness), skANI (taxonomic assignment against GTDB with ANI). It will also produce a Busco plot summary, a beeswarm plot of N50 and number of contigs, and an excel file with Quast, CheckM2 and skANI summaries. It will also output PDF and HTML reports with a summary and plots of all tools in the pipeline for all samples. The latest version of the scripts can be found at https://gitlab.ilvo.be/stevebaeyen/bacterial-assembly-qc-snakemake.</p>
Snakemake workflow for Nanopore-only bacterial assembly and QC
<p>This repository contains a Snakemake workflow tailored for assembling bacterial genomes from long-read data generated with R10.4.1 simplex reads from Oxford Nanopore Technologies and includes several QC steps on the resulting assemblies. The latest version of the scripts can be found at https://gitlab.ilvo.be/genomics/wgs/nanopore-only-bacterial-assembly-snakemake.</p>
Test fastq files for the BSA-seq Snakemake pipeline
<p>Rice genome reference fasta and individuals with high/low phenotype fastq files to be used to test the <a href="https://github.com/SilkeAllmannLab/snakemake_bsaseq">Snakemake BSA-seq pipeline</a> built to produce output files compatible for BSA-seq analysis using QTLSeqR.</p> <p>Genome file source: <a href="https://rapdb.dna.affrc.go.jp/download/irgsp1.html">https://rapdb.dna.affrc.go.jp/download/irgsp1.html </a></p> <p>Fastq file source: <a href="https://www.ncbi.nlm.nih.gov/bioproject/687818">https://www.ncbi.nlm.nih.gov/bioproject/687818</a></p> <p>Publication: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9123124/">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9123124/</a></p> <p> </p>
A snakemake toolkit for the batch assembly, annotation, and phylogenetic analysis of mitochondrial genomes and ribosomal genes from genome skims of museum collections
Open the record for dataset details and reuse information.
Snakemake workflow for Illumina bacterial assembly and QC v1.0.1
<p>This Illumina bacterial assembly snakemake repo is a snakemake workflow to assemble bacterial genomes from Illumina paired-end short-reads (typically 150bp); It also performs several QC steps on the reads and the resulting assemblies. Everything needed can be found in this repository (except for the GTDB reference database for taxonomic assembly classification and the Kraken2 database for taxonomical read classification, installation instructions provided in the README). The latest version of the scripts can be found at https://gitlab.ilvo.be/genomics/wgs/illumina-bacterial-assembly-snakemake and was updated to v1.0.1 with interactive and printer-friendly HTML and PDF reports summarising all QC metrics of reads and assemblies, tool versions used and a graphical workflow overview.</p>
Databases needed to run snakemake classifier
<p>Parsed Silva and Unite databases required as input for a snakemake workflow used to classify 18S and ITS1 sequences</p>
Snakemake report for manuscript "Orthanq: transparent and uncertainty-aware haplotype quantification with application in HLA-typing"
<p>For viewing the report, unzip the file and open index.html in your browser.</p>
Minified read mapping asignment dataset for use in Snakemake
<p>This is a minified version of the dataset used in the <a href="https://datacarpentry.org/wrangling-genomics/">Wranging Genomics Data Carpentries</a> lesson for use in the Galaxy Training Network materials on Snakemake and other workflow development.</p>
Staged Snakemake Workflow: stage
This is a a snapshot of the outputs of a Snakemake workflow
Fastq test files for Snakemake pipelines
<p>Sub-sampled Illumina fastq test files to develop and test RNA-seq Snakemake pipelines.</p> <p>Every file was subsampled to ~10% of its original content (ca 500,000 reads).</p> <p> </p>
Mapping SET1B Chromatin Interactions with DamID using DamMapper, a Comprehensive Snakemake Workflow
GEO Series GSE296995. Homo sapiens. 6 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
snakemake-metabolomics
<p>Metabolomics data for the snakemake-metabolomics workflow testing.</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.