bio-ecological-genomics-edna-metabarcoding

name	bio-ecological-genomics-edna-metabarcoding
description	Processes eDNA metabarcoding from raw paired-end reads to species tables, navigating ASV (DADA2, UNOISE3) vs OTU (swarm v2) decision (Callahan 2017 vs Schloss multi-copy-16S critique), marker/primer choice (Leray COI, MiFish 12S, 515F/806R 16S, ITS2) with primer-specific bias, OBITools3 v3 command-name break (obi stats plural; .tar.gz taxonomy), tag-jumping with dual-indexing (Schnell 2015; NovaSeq 10x MiSeq), decontam as screening-not-classifier (Davis 2018), read-counts-not-abundance critique (Lamb 2019), site-occupancy modeling (Ficetola 2015), Naive-Bayes calibration limits (Bokulich 2018), and eDNA decay (Strickler 2015). Use when going from raw eDNA FASTQ to species tables, picking marker + denoising pipeline, deciding whether read counts represent abundance, applying occupancy modeling, configuring OBITools3 v3, or interpreting decontam output. Not for clinical 16S microbiome (see microbiome/amplicon-processing).
tool_type	mixed
primary_tool	dada2

Version Compatibility

Reference examples tested with: DADA2 1.30+, cutadapt 4.7+, OBITools3 (Python 3), decontam 1.20+, microDecon 1.0+, occumb 1.0+, vsearch 2.27+, swarm 3.1+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• R: packageVersion('<pkg>') then ?function_name to verify parameters
• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

eDNA Metabarcoding

"Process eDNA samples to identify species present" -> Trim primers, denoise to ASVs (or cluster to OTUs), detect chimeras, assign taxonomy, filter contamination with negative controls AND DNA concentration, decompose tag-jumping artifacts, and quantify detection uncertainty via site-occupancy modeling. For the foundational eDNA-for-wildlife review, see Bohmann et al. 2014 Trends Ecol Evol 29:358-367.

• CLI: cutadapt for primer removal (linked-adapter mode)
• R: dada2::filterAndTrim() -> dada() -> assignTaxonomy() for ASV pipeline
• CLI: obi stats / obi clean / obi ecotag for OBITools3 (NOTE: v3 plural commands)
• R: decontam::isContaminant() for contamination screening
• R: occumb::occumb() for detection-corrected occurrence

The Single Most Important Modern Insight -- Read Counts Are NOT Abundance

Elbrecht & Leese 2015 PLoS One 10:e0130324 and Lamb et al. 2019 Mol Ecol 28:420-430 (meta-analysis) established that metabarcoding read counts have weak-to-moderate, taxon-specific, NONLINEAR correlation with biomass or DNA input. Primer-binding bias dominates; PCR replicates introduce stochasticity. Reporting read counts as abundance without mock-community calibration is malpractice. Modern practice: report PRESENCE/ABSENCE or relative abundance with explicit calibration; use multiple PCR replicates; apply site-occupancy models for detection correction.

A second cornerstone: the ASV-vs-OTU debate is taxon-specific, not universal. Callahan, McMurdie, Holmes 2017 ISME J 11:2639-2643 argued ASVs replace OTUs because modern denoising resolves single-nucleotide differences. Schloss 2021 mSphere 6:e00191-21 showed that for bacterial 16S with 1-15 intra-genomic rRNA copies, a single E. coli strain produces ~7 distinct ASVs, splitting bacterial genomes across artificial clusters. For COI metazoan metabarcoding, ASVs (DADA2/UNOISE3) are recommended; for bacterial 16S, ASVs inflate alpha-diversity and OTUs may be appropriate.

A third: decontam (Davis 2018) is a SCREENING tool, not a deterministic classifier. It flags candidates; biological plausibility check is required before deletion. The default threshold=0.1 over-flags in low-biomass data.

Algorithmic Taxonomy

Method	Output	Strength	Fails when
DADA2	Single-nucleotide ASVs	High resolution; learned error model; standard for COI/12S/18S/fungal-ITS	Small datasets (< 100 samples) for error learning; multi-copy bacterial rRNA
UNOISE3 (USEARCH/VSEARCH; Edgar 2016)	zOTUs (essentially ASVs)	Fast; algorithmic simplicity	Limited Linux/Mac binary distribution under license
Swarm v2 -d 1 --fastidious (Mahé 2015)	Abundance-weighted single-linkage OTUs	Modern OTU pipeline; better than legacy 97% UCLUST	OTUs by design (not single-nt resolution)
97% UCLUST	Classical OTUs	Legacy familiarity	Biologically arbitrary threshold; supersedes by DADA2/swarm
VSEARCH global pairwise	Taxonomic assignment via best-hit	Fast, transparent, no training	Conservative; mis-assigns sister species when ref incomplete
Naive Bayes (q2-feature-classifier, RDP)	Probabilistic taxonomic assignment	Probabilistic confidence; standard for 16S	Confidence values are scikit-learn calibrated, not true probabilities (Bokulich 2018)
SINTAX (Edgar)	Bootstrap-supported taxonomy	Fast; no training	Less accurate than Naive Bayes for divergent sequences
LCA (BASTA, MEGAN-LCA)	Lowest common ancestor of multiple hits	Conservative; never over-confident	Can over-merge to high taxonomic ranks
Phylogenetic placement (EPA-ng + gappa)	Position on reference tree	Most rigorous; phylogenetically explicit	10-100x slower; emerging not yet standard
decontam	Flagged contaminant candidates	Statistical screening of negative controls and DNA concentration patterns	Output is screening, not classification; needs biological-plausibility check
UCHIME3 (in DADA2/VSEARCH)	Chimera detection	Standard for de novo chimera removal	Some divergent chimeras escape

Decision Tree by Scenario

Scenario	Recommended approach	Why
Metazoan COI metabarcoding (water, gut content)	mlCOIintF/jgHCO2198 (Leray 2013) primers; DADA2 ASVs	Standard primer set; ASVs preserve single-nt resolution
Fish eDNA from water	MiFish-U/E (Miya 2015) 12S primers; DADA2 ASVs	Dominant eDNA fish marker globally
Freshwater macroinvertebrate bioassessment	BF1/BR1 freshwater-optimized COI primers	Higher primer-binding inclusivity for aquatic insects
Bacterial community 16S	515F/806R (V4) Parada modified; ASVs OR Swarm v2	Schloss 2021 caveat applies; ASVs may oversplit multi-copy rRNA
Fungal community ITS	ITS2 primers; DADA2 or UNITE pipeline	UNITE is curated for fungal ITS
Plant community DNA	trnL P6 loop (Taberlet 2007) for degraded DNA	Robust to degradation
Deciding ASV vs OTU	ASVs for COI/12S/18S/fungi; OTU consideration for 16S with multi-copy concern	Taxon-specific
NovaSeq library (patterned flow cell)	Heavier tag-jumping correction; expect 10x higher rates than MiSeq	Patterned-cell index hopping
Low-biomass eDNA (deep ocean, ancient)	decontam frequency + prevalence methods; explicit reagent-contamination check	Reagent contamination dominates
Quantitative comparison across samples	Mock-community calibration BEFORE reporting read counts	Without mock, read counts are biased estimators of biomass
Detection probability with replication	Site-occupancy models (occumb, eDNAoccupancy; Ficetola 2015)	Read counts alone underestimate occurrence; replicates correct
Taxonomic assignment for marker > 80% covered	Naive Bayes (q2-feature-classifier)	Probabilistic; well-supported
Taxonomic assignment for sparse reference	Phylogenetic placement (EPA-ng)	Robust to incomplete references
OBITools3 pipeline	obi stats (NOTE: plural), DMS-based, .tar.gz taxonomy	v3 syntax differs from v1

Primer Trimming with cutadapt

Goal: Remove primer sequences while discarding reads that lack primers, before quality filtering.

Approach: Use cutadapt linked-adapter mode with marker-specific 5' and 3' primer pairs. --discard-untrimmed removes reads lacking expected primers; min_overlap prevents false primer detection in random sequence regions.

# COI metazoan (Leray mlCOIintF / jgHCO2198 -> 313 bp)
cutadapt -g 'GGWACWGGWTGAACWGTWTAYCCYCC;min_overlap=20' \
         -G 'TAIACYTCIGGRTGICCRAARAAYCA;min_overlap=20' \
         --discard-untrimmed --pair-filter=any \
         -o trimmed_R1.fastq.gz -p trimmed_R2.fastq.gz \
         raw_R1.fastq.gz raw_R2.fastq.gz

# Fish 12S (MiFish-U -> 163-185 bp)
cutadapt -g 'GTCGGTAAAACTCGTGCCAGC;min_overlap=18' \
         -G 'CATAGTGGGGTATCTAATCCCAGTTTG;min_overlap=18' \
         --discard-untrimmed --pair-filter=any \
         -o trimmed_R1.fastq.gz -p trimmed_R2.fastq.gz \
         raw_R1.fastq.gz raw_R2.fastq.gz

# Fungal ITS2
cutadapt -g 'GTGAATCATCGAATCTTTGAAC;min_overlap=18' \
         -G 'TCCTCCGCTTATTGATATGC;min_overlap=18' \
         --discard-untrimmed --pair-filter=any \
         -o trimmed_R1.fastq.gz -p trimmed_R2.fastq.gz \
         raw_R1.fastq.gz raw_R2.fastq.gz

DADA2 ASV Pipeline

Goal: Denoise paired-end amplicon reads into exact amplicon sequence variants (ASVs) with chimera removal and reference-based taxonomy assignment, per Callahan et al. 2016 Nat Methods 13:581-583.

Approach: Filter to length/quality thresholds, learn error rates per dataset, run dada() to denoise, merge pairs, build sequence table, remove chimeras with UCHIME3-equivalent in DADA2, then assign taxonomy against the marker-appropriate reference DB. CRITICAL: primers must be removed (cutadapt) BEFORE filterAndTrim, OR the error model is corrupted.

library(dada2)

# CRITICAL: primer removal MUST precede filterAndTrim
# DADA2's error model assumes primer-free reads
fwd_reads <- sort(list.files('primer_trimmed/', pattern = '_R1', full.names = TRUE))
rev_reads <- sort(list.files('primer_trimmed/', pattern = '_R2', full.names = TRUE))
filt_fwd <- file.path('filtered', basename(fwd_reads))
filt_rev <- file.path('filtered', basename(rev_reads))

# Filter and trim
# maxEE=c(2,2): expected errors per read; tradeoff sensitivity/specificity
# truncLen: set from quality profile inspection; do not guess
out <- filterAndTrim(fwd_reads, filt_fwd, rev_reads, filt_rev,
                     maxN   maxEE    truncQ  
                     truncLen        
                     minLen   rm.phix   multithread  



err_fwd  learnErrorsfilt_fwd multithread  
err_rev  learnErrorsfilt_rev multithread  


dada_fwd  dadafilt_fwd err  err_fwd multithread  
dada_rev  dadafilt_rev err  err_rev multithread  


merged  mergePairsdada_fwd filt_fwd dada_rev filt_rev minOverlap  


seqtab  makeSequenceTablemerged





seqtab_nochim  removeBimeraDenovoseqtab method  
                                     multithread  
cat   seqtab_nochim  seqtab  









taxa  assignTaxonomyseqtab_nochim
                       
                       minBoot   multithread  

OBITools3 Pipeline — The v1 -> v3 Command Break

Goal: Process eDNA reads through the Unix-style OBITools v3 pipeline (Boyer et al. 2016 Mol Ecol Resour 16:176-182 introduced OBITools v1; v3 is the post-2018 Python 3 rewrite) with DMS-based sequence management.

Approach: v3 introduces a Database Management System (DMS) abstraction; sequences are imported into a DMS rather than read directly from FASTQ. Commands use spaces (e.g., obi stats plural, not obistat). Taxonomy import expects .tar.gz archive, not a directory.

# v1 -> v3 command-name changes (critical):
# v1: obistat       -> v3: obi stats
# v1: obigrep       -> v3: obi grep
# v1: obiuniq       -> v3: obi uniq
# v1: obitab        -> v3: obi annotate / obi export --tab-output (different semantics)
# v1: ngsfilter     -> v3: obi ngsfilter
# v1: taxdump dir   -> v3: .tar.gz archive

# Import paired FASTQ into DMS
obi import --fastq-input raw_R1.fastq.gz EDNA/reads1
obi import --fastq-input raw_R2.fastq.gz EDNA/reads2

# Paired-end alignment
obi alignpairedend -R EDNA/reads2 EDNA/reads1 EDNA/aligned

# Filter by alignment score and length
obi grep -p 'sequence["score"] >= 50' EDNA/aligned EDNA/filtered
obi grep -p 'len(sequence) >= 100 and len(sequence) <= 500' \
    EDNA/filtered EDNA/length_filtered

# Demultiplex (NGS filter file maps barcodes -> samples)
obi ngsfilter -t ngsfilter.txt -u EDNA/unassigned \
    EDNA/length_filtered EDNA/demux

# Dereplicate (obi uniq creates merged_sample attribute automatically)
obi uniq EDNA/demux EDNA/derep

# Remove suspected error singletons
obi grep -p 'sequence["count"] >= 2' EDNA/derep EDNA/no_singletons

# Denoise via obi clean
obi clean -s merged_sample -r 0.05 -H EDNA/no_singletons EDNA/denoised

# Taxonomy assignment against reference database
obi ecotag -R EDNA/refdb --taxonomy EDNA/taxonomy EDNA/denoised EDNA/assigned

# Export tab-separated species table
obi export --tab-output EDNA/assigned > species_table.tsv

Across most metabarcoding studies, 50-85% of ASVs cannot be assigned to species level due to incomplete references (Wangensteen et al. 2018 PeerJ 6:e4705 documented this for marine COI + 18S). Report this gap honestly; do not infer ecology from "unassigned" reads.

Tag-Jumping Mitigation — Schnell 2015 + NovaSeq Caveat

Goal: Detect and remove sequence-to-sample misassignments arising from chimeric library molecules with mismatched indices.

Approach: Use dual-indexing (different indices at both ends; cross-jumped pairs are discarded). Quantify residual tag-jumping rate from per-ASV cross-sample appearance and apply per-ASV abundance threshold filtering with metabaR::tagjumpslayer. For NovaSeq libraries, expect ~10x higher tag-jumping than MiSeq due to patterned flow cells.

library(metabaR)

# metabaR expects an metabarlist object (asv table + sample info + ngsfilter)
# tagjumpslayer applies per-ASV abundance-threshold filter
# threshold: 0.01 (1% of ASV total) is conservative; 0.001 for aggressive removal
# Adjust threshold higher for NovaSeq (~0.005-0.01) than MiSeq (~0.001-0.005)

# Quantify residual tag-jumping rate before filtering:
# Count reads in sample x ASV combinations that should be 0 by experimental design
# (e.g., samples explicitly excluded from a particular condition)
# That rate / total reads = empirical tag-jumping rate
# Report this rate in methods section

Contamination Screening with decontam

Goal: Identify candidate contaminant ASVs from negative controls and DNA-concentration patterns.

Approach: Use decontam::isContaminant with method='combined' when both DNA concentration AND negative controls are available. Treat flagged ASVs as SCREENING CANDIDATES; verify biological plausibility before deletion. The default threshold=0.1 is over-aggressive in low-biomass data.

library(decontam)

# Frequency method: contaminants more frequent at LOW DNA concentration
# Prevalence method: contaminants more frequent in negative controls
# Combined: uses both signals (most robust)

contam <- isContaminant(seqtab_nochim,
                        conc = dna_concentration,        # qPCR or Qubit per sample
                        neg = is_negative_control,       # logical: which samples are controls
                        method = 'combined',
                        threshold = 0.1)                 # default; lower for high-confidence calls

# CRITICAL: decontam output is SCREENING, not classification
# Manually inspect each flagged ASV: is the taxonomic assignment plausibly a reagent contaminant?
# Common reagent contaminants: Delftia, Sphingomonas, Burkholderia, Propionibacterium
flagged <- which(contam$contaminant)
cat('Decontam flagged', length(flagged), 'ASVs as candidates\n')

# After manual review, remove confirmed contaminants
confirmed_contam <- intersect(flagged, biological_plausibility_check_result)
seqtab_clean <- seqtab_nochim colnamesseqtab_nochim  confirmed_contam

Site-Occupancy Modeling — Correcting for Imperfect Detection

Goal: Estimate true species occurrence probabilities from replicated eDNA samples, accounting for false negatives in any single PCR replicate.

Approach: Fit a multi-species occupancy model via MCMC (Ficetola 2015 Mol Ecol Resour 15:543-556) on a 3D array of replicated read counts. Output: per-site, per-species occupancy probabilities corrected for detection.

library(occumb)

# y: 3D array [species, sites, replicates] of read counts
# spec_cov: species covariates (traits)
# site_cov: site covariates (env)
data_obj <- occumbData(y = count_array, spec_cov = species_covariates,
                       site_cov = site_covariates)

# Fit hierarchical occupancy model
# Requires JAGS installation
# n.iter >= 10000, n.burn >= 2500 for publication-quality posteriors
fit <- occumb(data = data_obj, n.chains = 4, n.iter = 10000,
              n.thin = 5, n.burn = 2500)

# Extract detection-corrected occupancy
summary(fit)

Per-Method Failure Modes

Reporting read counts as biomass without mock-community calibration

Trigger: Comparing read counts of two ASVs and reporting the ratio as a biomass / abundance estimate.

Mechanism: Primer-template binding affinity varies systematically across taxa; PCR amplification is non-linear (saturates); read counts have weak-to-moderate, NONLINEAR correlation with biomass (Elbrecht 2015; Lamb 2019).

Symptom: Reviewer asks "how is it known that reads = biomass?"; cross-study quantitative comparisons fail to replicate.

Fix: Either (a) restrict reporting to presence/absence; (b) report read counts as relative abundances with explicit caveat; or (c) include mock-community of known composition for primer-specific calibration. Do not silently equate reads with biomass.

NovaSeq tag-jumping with MiSeq-tuned filtering

Trigger: Applying tag-jumping filters calibrated on MiSeq libraries to NovaSeq data.

Mechanism: NovaSeq patterned flow cells have ~10x higher index hopping than MiSeq. MiSeq-calibrated thresholds (often ~0.001 fraction) are too permissive on NovaSeq data.

Symptom: Apparent rare-species detections in NovaSeq libraries do not replicate; per-ASV cross-sample appearance is unusually broad.

Fix: Use NovaSeq-appropriate tag-jumping thresholds (~0.005-0.01) and report the empirical tag-jumping rate from explicit-zero combinations.

decontam threshold over-aggressive in low-biomass data

Trigger: Applying default threshold = 0.1 to ASVs from open-ocean water, ancient sediments, or other dilute samples.

Mechanism: In low-biomass samples, the contaminant signal/background ratio approaches 1; decontam over-flags real but dilute biology as "contaminant" because the statistical pattern looks similar.

Symptom: Many ASVs flagged from low-biomass samples; taxonomic profile of "flagged contaminants" looks biologically realistic.

Fix: Lower threshold (0.05 or 0.01); always manually review flagged ASVs for biological plausibility; cite Salter 2014 BMC Biol 12:87 for the low-biomass reagent-contamination caveat.

Skipping primer removal before DADA2 filterAndTrim

Trigger: Running DADA2's filterAndTrim() on FASTQ files that still contain primer sequences.

Mechanism: DADA2 learns sequencing error from the empirical data; if primer sequences are present, they look like "perfect agreement" and corrupt the error model. ASVs are inferred with primer artifacts attached.

Symptom: DADA2 reports "phix-like contamination" (false; it's primers); ASVs start with the primer sequence; chimera rate elevated.

Fix: Always run cutadapt (or similar) BEFORE filterAndTrim. Verify with head of trimmed FASTQ that primer sequences are gone.

OBITools v3 commands with v1 syntax

Trigger: Running obistat or obigrep on a v3 install.

Mechanism: v1 used concatenated command names (obistat); v3 uses subcommand syntax with a space (obi stats — note plural).

Symptom: Bash error obistat: command not found; tutorial documentation does not match installed version.

Fix: Use obi <subcommand> syntax; consult obi --help for current command list. Taxonomy import requires .tar.gz archive, not unpacked directory.

Quantitative Thresholds

Threshold	Value	Source / rationale
DADA2 maxEE per read	2	Standard sensitivity/specificity balance
DADA2 chimera rate alarm	> 30% suggests library issues	Empirical convention
DADA2 minBoot for taxonomy	80 for genus; 50 for family	Standard confidence cutoffs
Tag-jumping filter MiSeq	0.001-0.005 fraction of ASV total	Schnell 2015
Tag-jumping filter NovaSeq	0.005-0.01 fraction of ASV total	Patterned-cell index hopping ~10x higher
decontam threshold	0.1 default; 0.05 for low-biomass	Davis 2018; reduce for dilute samples
Per-sample minimum reads	1000 (after filtering)	Below this rare-species detection unreliable
Singleton removal	count >= 2	Singletons often error-driven
Bootstrap nperm for tests	999	Standard permutation count
Occupancy model iterations	n.iter >= 10000, n.burn >= 2500	occumb default for stable posteriors
eDNA decay (20 deg C surface water)	half-life ~4-15 hours	Strickler 2015 Biol Conserv 183:85-92

Common errors

Error	Cause	Solution
obistat: command not found	OBITools v3 uses obi stats (plural)	Use v3 syntax
DADA2 error rate plot looks pathological	Primer sequences still in reads	Re-run cutadapt before filterAndTrim
Chimera rate > 30%	Library-prep issue or primer dimers	Inspect raw FASTQ; check PCR conditions
decontam flags many real species	Default threshold too aggressive for low-biomass	Lower threshold; manual review
Naive Bayes confidence 0.95 but species is wrong	scikit-learn-calibrated "confidence" not true probability	Use phylogenetic placement for borderline assignments
occumb JAGS not found error	JAGS not installed system-wide	Install JAGS (CRAN page has platform instructions)
eDNA detections do not replicate	Read counts treated as abundance	Switch to presence/absence; use mock-community calibration
MIDORI2 download path expired	Database updated; old URL gone	Check current MIDORI2 / MitoFish download page

References

• Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP (2016) DADA2. Nat Methods 13(7):581-583. doi:10.1038/nmeth.3869
• Callahan BJ, McMurdie PJ, Holmes SP (2017) Exact sequence variants should replace OTUs. ISME J 11(12):2639-2643. doi:10.1038/ismej.2017.119
• Edgar RC (2016) UNOISE2 / UNOISE3. bioRxiv preprint. doi:10.1101/081257
• Mahe F, Rognes T, Quince C, de Vargas C, Dunthorn M (2015) Swarm v2. PeerJ 3:e1420. doi:10.7717/peerj.1420
• Leray M, Yang JY, Meyer CP et al. (2013) mlCOIintF/jgHCO2198 metazoan COI primer. Front Zool 10:34. doi:10.1186/1742-9994-10-34
• Miya M, Sato Y, Fukunaga T et al. (2015) MiFish 12S fish eDNA primer. R Soc Open Sci 2(7):150088. doi:10.1098/rsos.150088
• Schnell IB, Bohmann K, Gilbert MTP (2015) Tag jumps illuminated. Mol Ecol Resour 15(6):1289-1303. doi:10.1111/1755-0998.12402
• Davis NM, Proctor DM, Holmes SP, Relman DA, Callahan BJ (2018) decontam. Microbiome 6:226. doi:10.1186/s40168-018-0605-2
• Boyer F, Mercier C, Bonin A, Le Bras Y, Taberlet P, Coissac E (2016) OBITools. Mol Ecol Resour 16(1):176-182. doi:10.1111/1755-0998.12428
• Elbrecht V, Leese F (2015) DNA-based ecosystem quantification critique. PLoS One 10(7):e0130324. doi:10.1371/journal.pone.0130324
• Lamb PD, Hunter E, Pinnegar JK, Creer S, Davies RG, Taylor MI (2019) How quantitative is metabarcoding: meta-analysis. Mol Ecol 28(2):420-430. doi:10.1111/mec.14920
• Ficetola GF, Pansu J, Bonin A et al. (2015) Replication levels and false presences in eDNA. Mol Ecol Resour 15(3):543-556. doi:10.1111/1755-0998.12338
• Wangensteen OS, Palacin C, Guardiola M, Turon X (2018) COI + 18S marine metabarcoding. PeerJ 6:e4705. doi:10.7717/peerj.4705
• Strickler KM, Fremier AK, Goldberg CS (2015) eDNA degradation kinetics. Biol Conserv 183:85-92. doi:10.1016/j.biocon.2014.11.038
• Bokulich NA, Kaehler BD, Rideout JR et al. (2018) Optimizing taxonomic classification with q2-feature-classifier. Microbiome 6:90. doi:10.1186/s40168-018-0470-z
• Bohmann K, Evans A, Gilbert MTP et al. (2014) eDNA for wildlife and biodiversity. Trends Ecol Evol 29(6):358-367. doi:10.1016/j.tree.2014.04.003
• Schloss PD (2021) Amplicon sequence variants artificially split bacterial genomes into separate clusters. mSphere 6(4):e00191-21. doi:10.1128/mSphere.00191-21
• Salter SJ, Cox MJ, Turek EM et al. (2014) Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol 12:87. doi:10.1186/s12915-014-0087-z

Related Skills

• ecological-genomics/biodiversity-metrics - Diversity analysis from species occurrence tables (Hill numbers, beta partition)
• ecological-genomics/community-ecology - Environmental gradient analysis of community composition (PERMANOVA + PERMDISP, ordination)
• microbiome/amplicon-processing - 16S clinical microbiome alternative pipeline
• read-qc/quality-reports - Upstream read-quality assessment before primer trimming
• database-access/entrez-fetch - Retrieve reference sequences for custom taxonomy databases