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SPIKEPIPE: A metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and abundances using DNA barcodes or mitogenomes
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Effects of food abundance and early clutch predation on reproductive timing in a high Arctic shorebird exposed to advancements in arthropod abundance
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Drivers of inter-annual variation and long-term change in High-Arctic spider species abundances
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Foreword: Synthesis of the Greenland Ecosystem Monitoring program
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Interaction webs in arctic ecosystems: Determinants of arctic change?
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Rapid advancement of spring in the High Arctic
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Degradation and dispersion limit environmental DNA detection of rare amphibians in wetlands: Increasing efficacy of sampling designs
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The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems
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A method for simultaneous measurement of soil bacterial abundances and community composition via 16S rRNA gene sequencing
inferredcites →https://doi.org/10.1016/j.tree.2014.04.003openalex-snapshot
Environmental DNA for wildlife biology and biodiversity monitoring
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Next-Generation Global Biomonitoring: Large-scale, Automated Reconstruction of Ecological Networks
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Implementation options for DNA-based identification into ecological status assessment under the European Water Framework Directive
inferredcites →https://doi.org/10.1016/j.ympev.2012.08.023openalex-snapshot
MITOS: Improved de novo metazoan mitochondrial genome annotation
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Shorter flowering seasons and declining abundance of flower visitors in a warmer Arctic
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Connecting Earth observation to high-throughput biodiversity data
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Metazoan mitochondrial gene sequence reference datasets for taxonomic assignment of environmental samples
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DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies
inferredcites →https://doi.org/10.1080/15230430.2017.1415624openalex-snapshot
Spatiotemporal snowmelt patterns within a high Arctic landscape, with implications for flora and fauna
inferredcites →https://doi.org/10.1086/652373openalex-snapshot
Conceptual Synthesis in Community Ecology
inferredcites →https://doi.org/10.1089/cmb.2013.0084openalex-snapshot
Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot
BEDTools: a flexible suite of utilities for comparing genomic features
inferredcites →https://doi.org/10.1093/bioinformatics/bts174openalex-snapshot
IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
inferredcites →https://doi.org/10.1093/bioinformatics/btu077openalex-snapshot
SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads
inferredcites →https://doi.org/10.1093/bioinformatics/btv290openalex-snapshot
BFC: correcting Illumina sequencing errors
inferredcites →https://doi.org/10.1093/bioinformatics/bty191openalex-snapshot
Minimap2: pairwise alignment for nucleotide sequences
inferredcites →https://doi.org/10.1093/czoolo/60.2.243openalex-snapshot
Phenology of high-arctic butterflies and their floral resources: Species-specific responses to climate change
inferredcites →https://doi.org/10.1093/molbev/msv111openalex-snapshot
Soup to Tree: The Phylogeny of Beetles Inferred by Mitochondrial Metagenomics of a Bornean Rainforest Sample
inferredcites →https://doi.org/10.1093/nar/gkt371openalex-snapshot
Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach
inferredcites →https://doi.org/10.1093/nar/gkw955openalex-snapshot
NOVOPlasty: de novo assembly of organelle genomes from whole genome data
inferredcites →https://doi.org/10.1093/nar/gky1022openalex-snapshot
The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications
inferredcites →https://doi.org/10.1098/rsos.171503openalex-snapshot
Differential arthropod responses to warming are altering the structure of Arctic communities
inferredcites →https://doi.org/10.1111/1755-0998.12355openalex-snapshot
Universal and blocking primer mismatches limit the use of high‐throughput DNA sequencing for the quantitative metabarcoding of arthropods
inferredcites →https://doi.org/10.1111/1755-0998.12472openalex-snapshot
Mitochondrial capture enriches mito‐DNA 100 fold, enabling PCR‐free mitogenomics biodiversity analysis
inferredcites →https://doi.org/10.1111/1755-0998.12489openalex-snapshot
Establishing a community‐wide DNA barcode library as a new tool for arctic research
inferredcites →https://doi.org/10.1111/1755-0998.12740openalex-snapshot
Genetic monitoring of open ocean biodiversity: An evaluation of DNA metabarcoding for processing continuous plankton recorder samples
inferredcites →https://doi.org/10.1111/1755-0998.12755openalex-snapshot
Give me a sample of air and I will tell which species are found from your region: Molecular identification of fungi from airborne spore samples
inferredcites →https://doi.org/10.1111/1755-0998.12888openalex-snapshot
Performance of amplicon and shotgun sequencing for accurate biomass estimation in invertebrate community samples
inferredcites →https://doi.org/10.1111/1755-0998.12895openalex-snapshot
Minimizing polymerase biases in metabarcoding
inferredcites →https://doi.org/10.1111/1755-0998.12928openalex-snapshot
Capture enrichment of aquatic environmental DNA: A first proof of concept
inferredcites →https://doi.org/10.1111/2041-210x.12376openalex-snapshot
Validating the power of mitochondrial metagenomics for community ecology and phylogenetics of complex assemblages
inferredcites →https://doi.org/10.1111/2041-210x.12416openalex-snapshot
High‐throughput monitoring of wild bee diversity and abundance via mitogenomics
inferredcites →https://doi.org/10.1111/2041-210x.12942openalex-snapshot
Better together: Integrating and fusing multispectral and radar satellite imagery to inform biodiversity monitoring, ecological research and conservation science
inferredcites →https://doi.org/10.1111/ecog.02261openalex-snapshot
An ecological function in crisis? The temporal overlap between plant flowering and pollinator function shrinks as the Arctic warms
inferredcites →https://doi.org/10.1111/ecog.02747openalex-snapshot
Declining diversity and abundance of High Arctic fly assemblages over two decades of rapid climate warming
inferredcites →https://doi.org/10.1111/ele.12162openalex-snapshot
Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding
inferredcites →https://doi.org/10.1111/ele.13092openalex-snapshot
Animal Sound Identifier ( ASI ): software for automated identification of vocal animals
inferredcites →https://doi.org/10.1111/j.1755-0998.2011.03067.xopenalex-snapshot
BOLD’s role in barcode data management and analysis: a response
inferredcites →https://doi.org/10.1111/j.2041-210x.2012.00198.xopenalex-snapshot
Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring
inferredcites →https://doi.org/10.1111/mec.14478openalex-snapshot
Scaling up: A guide to high‐throughput genomic approaches for biodiversity analysis
inferredcites →https://doi.org/10.1111/mec.14734openalex-snapshot
Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data?
inferredcites →https://doi.org/10.1111/mec.14776openalex-snapshot
The choice of universal primers and the characteristics of the species mixture determine when DNA metabarcoding can be quantitative
inferredcites →https://doi.org/10.1111/mec.14920openalex-snapshot
How quantitative is metabarcoding: A meta‐analytical approach
inferredcites →https://doi.org/10.1111/oik.05074openalex-snapshot
Between‐year changes in community composition shape species’ roles in an Arctic plant–pollinator network
inferredcites →https://doi.org/10.1186/1471-2105-13-s4-s1openalex-snapshot
Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee
inferredcites →https://doi.org/10.1186/1471-2105-13-s6-s1openalex-snapshot
Exploiting sparseness in de novo genome assembly
inferredcites →https://doi.org/10.1186/1472-6785-12-28openalex-snapshot
Assessing biodiversity of a freshwater benthic macroinvertebrate community through non-destructive environmental barcoding of DNA from preservative ethanol
inferredcites →https://doi.org/10.1186/2047-217x-2-4openalex-snapshot
Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification
inferredcites →https://doi.org/10.1186/s13059-019-1632-4openalex-snapshot
Skmer: assembly-free and alignment-free sample identification using genome skims
inferredcites →https://doi.org/10.1186/s13742-016-0120-yopenalex-snapshot
Mitochondrial metagenomics: letting the genes out of the bottle
inferredcites →https://doi.org/10.1186/s40168-018-0491-7openalex-snapshot
Absolute quantitation of microbiota abundance in environmental samples
inferredcites →https://doi.org/10.1371/journal.pone.0000272openalex-snapshot
DNA Extraction from Dry Museum Beetles without Conferring External Morphological Damage
inferredcites →https://doi.org/10.1371/journal.pone.0013102openalex-snapshot
Use of ITS2 Region as the Universal DNA Barcode for Plants and Animals
inferredcites →https://doi.org/10.1371/journal.pone.0066213openalex-snapshot
A DNA-Based Registry for All Animal Species: The Barcode Index Number (BIN) System
inferredcites →https://doi.org/10.1371/journal.pone.0112963openalex-snapshot
Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
inferredcites →https://doi.org/10.14806/ej.17.1.200openalex-snapshot
Cutadapt removes adapter sequences from high-throughput sequencing reads
inferredcites →https://doi.org/10.5281/zenodo.15145663openalex-snapshot
Table 1 in A new Gammarus species from Xinjiang Uygur Autonomous Region (China) with a key to Xinjiang freshwater gammarids (Crustacea, Amphipoda, Gammaridae)
inferredcites →https://doi.org/10.6084/m9.figshare.963153.v1openalex-snapshot
Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEM
inferredcites →https://doi.org/10.7717/peerj.6174openalex-snapshot
Kelpie: generating full-length ‘amplicons’ from whole-metagenome datasets
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1007/s10531-020-01980-0openalex-snapshot
Applications of environmental DNA (eDNA) in ecology and conservation: opportunities, challenges and prospects
inferred← citeshttps://doi.org/10.1093/gigascience/giz092openalex-snapshot
Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance
inferred← citeshttps://doi.org/10.1111/1755-0998.13057openalex-snapshot
SPIKEPIPE: A metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and intraspecific abundance change using DNA barcodes or mitogenomes
inferred← citeshttps://doi.org/10.1111/2041-210x.13265openalex-snapshot
Semi‐quantitative characterisation of mixed pollen samples using MinION sequencing and Reverse Metagenomics (RevMet)
inferred← citeshttps://doi.org/10.1111/gcb.15297openalex-snapshot
Parasitoids indicate major climate‐induced shifts in arctic communities
inferred← citeshttps://doi.org/10.33624/2587-9367-2023-1(9)-8-17openalex-snapshot
Metagenomic analysis as a tool for studying and monitoring biological diversity in the Arctic Seas
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