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Privacy-aware community infrastructureGregory D. Edgecombe, Liam M. Crowley, Darwin Tree of Life Barcoding Collective, Tree of Life Core Informatics collective
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MitoFinder: efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics.
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DNA barcoding SOPs for the Darwin Tree of Life project.
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Studies on the millipedes of a Devon oak wood.
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Drost HG: Sensitive protein alignments at Tree-of-Life scale using DIAMOND.
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Genomes on a Tree (GoaT): a versatile, scalable search engine for genomic and sequencing project metadata across the eukaryotic Tree of Life [version 1; peer review: 2 approved].
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Confidence 100%
ror
Confidence 99%
europepmc
Confidence 96%
openalex
Confidence 95%
unpaywall
Confidence 95%
doaj
Confidence 92%
datacite
Confidence 0%
BlobToolKit – interactive quality assessment of genome assemblies.
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Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm.
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BioContainers: an open-source and community-driven framework for software standardization.
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Sanger Tree of Life sample homogenisation: PowerMash.
10.17504/protocols.io.5qpvo3r19v4o/v1
Sanger Tree of Life wet laboratory protocol collection V.1.
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Nextflow enables reproducible computational workflows.
10.1038/nbt.3820 · 2017
JBrowse 2: a modular genome browser with views of synteny and structural variation.
10.1186/s13059-023-02914-z · 2023
Sanger Tree of Life RNA extraction: automated MagMax ™ mirVana.
10.17504/protocols.io.6qpvr36n3vmk/v1 · 2023
MultiQC: summarize analysis results for multiple tools and samples in a single report.
10.1093/bioinformatics/btw354 · 2016
The nf-core framework for community-curated bioinformatics pipelines.
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Identifying and removing haplotypic duplication in primary genome assemblies.
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Das Paarungsverhalten von Cylindroiulus punctatus leach.
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PretextView (Paired REad TEXTure Viewer): a desktop application for viewing pretext contact maps.
2022
Significantly improving the quality of genome assemblies through curation.
10.1093/gigascience/giaa153 · 2021
Defensive secretions of millipedes: more than just a product of melting point decrease?
2000
Sanger Tree of Life sample preparation: triage and dissection.
10.17504/protocols.io.x54v9prmqg3e/v1 · 2023
Genome of the rusty millipede, Trigonoiulus corallinus, illuminates diplopod, myriapod and arthropod evolution.
10.1093/gbe/evv070 · 2015
HiGlass: web-based visual exploration and analysis of genome interaction maps.
10.1186/s13059-018-1486-1 · 2018
Atlas of European millipedes 2: order Julida (Class Diplopoda).
10.5852/ejt.2017.346 · 2017
Singularity: scientific containers for mobility of compute.
10.1371/journal.pone.0177459 · 2017
Specimen and sample metadata standards for biodiversity genomics: a proposal from the Darwin Tree of Life project [version 1; peer review: 2 approved with reservations].
10.12688/wellcomeopenres.17605.1 · 2022
Atlas of the millipedes (Diplopoda) of Britain and Ireland. Sofia: Pensoft
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Minimap2: pairwise alignment for nucleotide sequences.
10.1093/bioinformatics/bty191 · 2018
BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes.
10.1093/molbev/msab199 · 2021
Docker: lightweight Linux containers for consistent development and deployment.
2014
10.1163/9789004630383_015
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Sanger Tree of Life HMW DNA fragmentation: Covaris g-TUBE for ULI PacBio.
10.17504/protocols.io.q26g7pm81gwz/v1 · 2023
YaHS: Yet another Hi-C Scaffolding tool.
10.1093/bioinformatics/btac808 · doi-reference
Efficient architecture-aware acceleration of BWA-MEM for multicore systems.
10.1109/ipdps.2019.00041 · doi-reference
MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads.
10.1186/s12859-023-05385-y · doi-reference
A DNA barcoding framework for taxonomic verification in the Darwin Tree of Life project [version 1; peer review: 2 approved].
10.12688/wellcomeopenres.21143.1 · doi-reference
Sanger Tree of Life fragmented DNA clean up: manual SPRI.
10.17504/protocols.io.kxygx3y1dg8j/v1 · doi-reference
Myriapod genomes reveal ancestral horizontal gene transfer and hormonal gene loss in millipedes.
10.1038/s41467-022-30690-0 · doi-reference
Sanger Tree of Life HMW DNA extraction: automated MagAttract v.1.
10.17504/protocols.io.x54v9p2z1g3e/v1 · doi-reference
Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies.
10.1186/s13059-020-02134-9 · doi-reference
Towards complete and error-free genome assemblies of all vertebrate species.
10.1038/s41586-021-03451-0 · doi-reference
A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.
10.1016/j.cell.2014.11.021 · doi-reference
GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes.
10.1038/s41467-020-14998-3 · doi-reference
Millipede genomes reveal unique adaptations during myriapod evolution.
10.1371/journal.pbio.3000636 · doi-reference
sanger-tol/treeval v1.0.0 – Ancient Atlantis.
10.5281/zenodo.10047654 · doi-reference
DToL taxon-specific standard operating procedure for the terrestrial and freshwater arthropods working group.
10.17504/protocols.io.261gennyog47/v1 · doi-reference
