Research graph
References from The genome sequence of the eyed flat-backed millipede, Nanogona polydesmoides (Leach, 1814). Local targets link to admitted publications; unresolved targets remain external evidence.
Mirny LA: Cooler: scalable storage for Hi-C data and other genomically labeled arrays.
10.1093/bioinformatics/btz540 · 2020 · External reference
Mito Finder: efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics.
10.1111/1755-0998.13160 · 2020 · External reference
Basic Local Alignment Search Tool.
10.1016/s0022-2836(05)80360-2 · 1990 · External reference
Uni Prot: the Universal Protein Knowledgebase in 2023.
10.1093/nar/gkac1052 · 2023 · External reference
DNA barcoding SOPs for the Darwin Tree of Life project.
10.17504/protocols.io.261ged91jv47/v1 · 2023 · External reference
10.1163/9789004627604
10.1163/9789004627604 · 1985 · External reference
Drost HG: Sensitive protein alignments at Tree-of-Life scale using DIAMOND.
10.1038/s41592-021-01101-x · 2021 · External reference
Genomes on a Tree (Goa T): a versatile, scalable search engine for genomic and sequencing project metadata across the eukaryotic Tree of Life [version 1; peer review: 2 approved].
10.12688/wellcomeopenres.18658.1 · 2023 · External reference
Blob Tool Kit – interactive quality assessment of genome assemblies.
10.1534/g3.119.400908 · 2020 · External reference
Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm.
10.1038/s41592-020-01056-5 · 2021 · External reference
Meta Invert: a new soil invertebrate genome resource provides insights into below-ground biodiversity and evolution.
10.21203/rs.3.rs-2706746/v1 · 2023 · External reference
A sampling strategy for genome sequencing the British terrestrial arthropod fauna [version 1; peer review: 2 approved].
10.12688/wellcomeopenres.18925.1 · 2023 · External reference
Bio Containers: an open-source and community-driven framework for software standardization.
10.1093/bioinformatics/btx192 · 2017 · External reference
Twelve years of SAMtools and BCFtools.
10.1093/gigascience/giab008 · 2021 · External reference
ome questions about the evolution of life-history traits in Diplopoda.
1992 · External reference
Nanogona polyesmoides (Leach, 1815) – new for the German fauna (Diplopoda, Chordeumatida, Craspedosomatidae).
2010 · External reference
Sanger Tree of Life sample homogenisation: Power Mash. protocols.io.
10.17504/protocols.io.5qpvo3r19v4o/v1 · External reference
Sanger Tree of Life wet laboratory protocol collection V.1. protocols.io.
10.17504/protocols.io.8epv5xxy6g1b/v1 · External reference
Nextflow enables reproducible computational workflows.
10.1038/nbt.3820 · 2017 · External reference
JBrowse 2: a modular genome browser with views of synteny and structural variation.
10.1186/s13059-023-02914-z · 2023 · External reference
Sanger Tree of Life RNA extraction: automated Mag Max ™ mir Vana. protocols.io.
10.17504/protocols.io.6qpvr36n3vmk/v1 · 2023 · External reference
Multi QC: summarize analysis results for multiple tools and samples in a single report.
10.1093/bioinformatics/btw354 · 2016 · External reference
The nf-core framework for community-curated bioinformatics pipelines.
10.1038/s41587-020-0439-x · 2020 · External reference
Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs.
10.1093/bioinformatics/btac460 · 2022 · External reference
Bioconda: sustainable and comprehensive software distribution for the life sciences.
10.1038/s41592-018-0046-7 · 2018 · External reference
Pretext View (Paired REad TEXTure Viewer): a desktop application for viewing pretext contact maps.
2022 · External reference
Significantly improving the quality of genome assemblies through curation.
10.1093/gigascience/giaa153 · 2021 · External reference
Sanger Tree of Life sample preparation: triage and dissection. protocols.io.
10.17504/protocols.io.x54v9prmqg3e/v1 · 2023 · External reference
Genome of the rusty millipede, Trigoniulus corallinus, illuminates diplopod, myriapod, and arthropod evolution.
10.1093/gbe/evv070 · 2015 · External reference
HiGlass: web-based visual exploration and analysis of genome interaction maps.
10.1186/s13059-018-1486-1 · 2018 · External reference
The Belgian millipede fauna.
2004 · External reference
Singularity: scientific containers for mobility of compute.
10.1371/journal.pone.0177459 · 2017 · External reference
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 · External reference
Atlas of the millipedes (Diplopoda) of Britain and Ireland. Sofia: Pensoft
2006 · External reference
Minimap 2: pairwise alignment for nucleotide sequences.
10.1093/bioinformatics/bty191 · 2018 · External reference
A millipede’s tent.
1931 · External reference
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 · External reference
Docker: lightweight Linux containers for consistent development and deployment.
2014 · External reference
Sanger Tree of Life HMW DNA fragmentation: Covaris g-TUBE for ULI Pac Bio.
10.17504/protocols.io.q26g7pm81gwz/v1 · 2023 · External reference
DToL Taxon-specific standard operating procedure for the terrestrial and freshwater arthropods working group.
10.17504/protocols.io.261gennyog47/v1 · 2022 · External reference
sanger-tol/treeval v1.0.0 – Ancient Atlantis.
10.5281/zenodo.10047654 · 2023 · External reference
Millipede genomes reveal unique adaptations during myriapod evolution.
10.1371/journal.pbio.3000636 · 2020 · External reference
BEDTools: a flexible suite of utilities for comparing genomic features.
10.1093/bioinformatics/btq033 · 2010 · External reference
Genome Scope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes.
10.1038/s41467-020-14998-3 · 2020 · External reference
A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.
10.1016/j.cell.2014.11.021 · 2014 · External reference
Towards complete and error-free genome assemblies of all vertebrate species.
10.1038/s41586-021-03451-0 · 2021 · External reference
Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies.
10.1186/s13059-020-02134-9 · 2020 · External reference
Sanger Tree of Life HMW DNA extraction: automated Mag Attract v. 1. protocols.io.
10.17504/protocols.io.x54v9p2z1g3e/v1 · 2023 · External reference
Myriapod genomes reveal ancestral horizontal gene transfer and hormonal gene loss in millipedes.
10.1038/s41467-022-30690-0 · 2022 · External reference
Sanger Tree of Life fragmented DNA clean up: manual SPRI. protocols.io.
10.17504/protocols.io.kxygx3y1dg8j/v1 · 2023 · External 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 · 2024 · External reference
Mito HiFi: a python pipeline for mitochondrial genome assembly from Pac Bio high fidelity reads.
10.1186/s12859-023-05385-y · 2023 · External reference
10.1109/ipdps.2019.00041
10.1109/ipdps.2019.00041 · 2019 · External reference
YaHS: Yet another Hi-C Scaffolding tool.
10.1093/bioinformatics/btac808 · 2023 · External reference
