Model type
Study-specific predictive method; this record is the paper-specific evaluated configuration.
Pipeline
Lazypipe-nt
LAZYPIPE is an automated assembly and taxonomic-profiling workflow for virus discovery in sequencing libraries.
Sources
Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types · 2. Materials and methods/2.2 Unix pipeline for assembly, taxonomic profiling and binning of NGS data (paragraph 1); Abstract (paragraph 1)How it worksEvaluated procedure (conceptual)
Conceptual input–method–output guide. Check the procedure text and linked evaluation for fitted components, additional inputs and exact settings.
Sources
Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types · 2. Materials and methods/2.2 Unix pipeline for assembly, taxonomic profiling and binning of NGS data (paragraph 3); 2. Materials and methods/2.2 Unix pipeline for assembly, taxonomic profiling and binning of NGS data (paragraph 5)Overview
Biological inputs
NGS libraries from host-associated or environmental samples
Sources
Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types · Abstract (paragraph 1); 3. Results/3.3 Novel virome sequences from mink faecal samples (paragraph 1)Outputs
Assembled contigs and taxonomic/viral profiles
Sources
Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types · 1. Introduction (paragraph 6); 3. Results/3.1 Excellent recall and precision for both simulated and real datasets (paragraph 3)Access
The paper provides the source and manual at https://bitbucket.org/plyusnin/lazypipe/ and https://www.helsinki.fi/en/projects/lazypipe. This records the published access route, not a live-service availability guarantee.
Sources
Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types · Materials and methods / Unix pipeline for assembly, taxonomic profiling and binning of NGS datalimited source coverage · Automated source review, 2026-09-16. All specifications and missing details
Evaluations and results
1 evaluation · 1 result. Different protocols are not a single leaderboard.
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Pipeline: Lazypipe-nt | Task: Simulated metagenome virus-taxon retrieval Dataset: Simulated viral metagenome | 0.932 Genus-level F1 unitless · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceLazypipe-nt: Simulated metagenome virus-taxon retrieval Genus-rank viral taxon retrieval. Aggregation: Not reported Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types · Table 1, Lazypipe-nt / Genus row, F column |
Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.
Use this model
How it works, versions and access
How it works
How the evaluated method works
Unix-based C++, Perl and R components assemble reads and assign taxonomy. The nt-labelled configuration is the nucleotide-database variant, distinct from other database choices in the paper.
Sources
Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types · 2. Materials and methods/2.2 Unix pipeline for assembly, taxonomic profiling and binning of NGS data (paragraph 3); 2. Materials and methods/2.2 Unix pipeline for assembly, taxonomic profiling and binning of NGS data (paragraph 5)What was evaluated
The linked evaluation record identifies Lazypipe-nt: Simulated metagenome virus-taxon retrieval. Its dataset, split, adaptation and evidence origin remain attached to the reported results.
Sources
Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types · The named evaluation’s methods and comparison table; exact preserved evaluation IDs: evaluation-lit-b3-021Strengths, limitations and unresolved questions
Strengths and limitations
Strengths and considerations
- Combines assembly with annotation for inspection of known and potentially novel viral sequences.
Sources
Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types · 4. Discussion (paragraph 1); 4. Discussion (paragraph 4)
Limitations and conditions
- Results depend on library preprocessing, assembly and reference databases; the pipeline is not a single learned model.
Sources
Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types · 2. Materials and methods/2.2 Unix pipeline for assembly, taxonomic profiling and binning of NGS data (paragraph 8); 2. Materials and methods/2.3 Benchmarking performance (paragraph 1)
Profile review details
Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction.
Stable record: reported-model-8cb3dd4e9f5b10Specifications
Inputs, training, access and other details
Explanatory profile: limited source coverage · Automated source review, 2026-09-16. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.
| Property | Description and evidence |
|---|---|
| Model type | Study-specific predictive method; this record is the paper-specific evaluated configuration.SourcesNovel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types · 2. Materials and methods/2.2 Unix pipeline for assembly, taxonomic profiling and binning of NGS data (paragraph 3); 2. Materials and methods/2.2 Unix pipeline for assembly, taxonomic profiling and binning of NGS data (paragraph 5) |
| Architecture / procedure | Unix-based C++, Perl and R components assemble reads and assign taxonomy. The nt-labelled configuration is the nucleotide-database variant, distinct from other database choices in the paper.SourcesNovel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types · 2. Materials and methods/2.2 Unix pipeline for assembly, taxonomic profiling and binning of NGS data (paragraph 3); 2. Materials and methods/2.2 Unix pipeline for assembly, taxonomic profiling and binning of NGS data (paragraph 5) |
| Biological inputs | NGS libraries from host-associated or environmental samplesSourcesNovel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types · Abstract (paragraph 1); 3. Results/3.3 Novel virome sequences from mink faecal samples (paragraph 1) |
| Outputs | Assembled contigs and taxonomic/viral profilesSourcesNovel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types · 1. Introduction (paragraph 6); 3. Results/3.1 Excellent recall and precision for both simulated and real datasets (paragraph 3) |
| Parameters | Not applicable to a neural parameter count: this pipeline assembles, aligns and bins reads/contigs. · Not applicableSourcesNovel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types · 2. Materials and methods/2.2 Unix pipeline for assembly, taxonomic profiling and binning of NGS data (paragraph 4); 2. Materials and methods/2.2 Unix pipeline for assembly, taxonomic profiling and binning of NGS data (paragraph 8) |
| Known versions / configuration | Lazypipe-nt is the comparison-table label; that label does not specify an immutable weight revision. · Not reported in inspected sourcesSourcesNovel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types · Model identification in the comparison table and corresponding Methods; immutable checkpoint revision is not supplied by the table label. |
| Training data / fitting | No task-specific neural fitting: assembled contigs are classified by Centrifuge against NCBI nt. The benchmark removes alignments with less than 60 nucleotides matched; a dated NCBI nt snapshot is not identified in this passage.SourcesNovel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types · Materials and methods / Unix pipeline; Benchmarking performance |
| Context limits | Not applicable to a learned token window; paired-end reads and their assembled contigs are the analysed input. · Not applicableSourcesNovel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types · 1. Introduction (paragraph 6); 2. Materials and methods/2.2 Unix pipeline for assembly, taxonomic profiling and binning of NGS data (paragraph 4) |
| Access | The paper provides the source and manual at https://bitbucket.org/plyusnin/lazypipe/ and https://www.helsinki.fi/en/projects/lazypipe. This records the published access route, not a live-service availability guarantee.SourcesNovel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types · Materials and methods / Unix pipeline for assembly, taxonomic profiling and binning of NGS data |
| Code licence | No explicit code licence was established from the paper’s availability statement and inspected repository-root documentation. · Not reported in inspected sourcesSourcesNovel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types · 1. Introduction (paragraph 4); 4. Discussion (paragraph 1) |
| Weights licence | The inspected model-access documentation does not explicitly identify terms for this exact evaluated checkpoint or fitted head; repository code terms are shown separately. · Not reported in inspected sourcesSourcesNovel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types · 1. Introduction (paragraph 4); 4. Discussion (paragraph 1) |
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
19 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Conceptual input–method–output guide. Check the procedure text and linked evaluation for fitted components, additional inputs and exact settings. Individual claims | Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types 2. Materials and methods/2.2 Unix pipeline for assembly, taxonomic profiling and binning of NGS data (paragraph 3); 2. Materials and methods/2.2 Unix pipeline for assembly, taxonomic profiling and binning of NGS data (paragraph 5) Version: version of record | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Diagram steps
| Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types 2. Materials and methods/2.2 Unix pipeline for assembly, taxonomic profiling and binning of NGS data (paragraph 3); 2. Materials and methods/2.2 Unix pipeline for assembly, taxonomic profiling and binning of NGS data (paragraph 5) Version: version of record | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Evaluated procedure (conceptual) Individual claims | Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types 2. Materials and methods/2.2 Unix pipeline for assembly, taxonomic profiling and binning of NGS data (paragraph 3); 2. Materials and methods/2.2 Unix pipeline for assembly, taxonomic profiling and binning of NGS data (paragraph 5) Version: version of record | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Model type Study-specific predictive method; this record is the paper-specific evaluated configuration. Individual claims | Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types 2. Materials and methods/2.2 Unix pipeline for assembly, taxonomic profiling and binning of NGS data (paragraph 3); 2. Materials and methods/2.2 Unix pipeline for assembly, taxonomic profiling and binning of NGS data (paragraph 5) Version: version of record | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Architecture / procedure Unix-based C++, Perl and R components assemble reads and assign taxonomy. The nt-labelled configuration is the nucleotide-database variant, distinct from other database choices in the paper. Individual claims | Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types 2. Materials and methods/2.2 Unix pipeline for assembly, taxonomic profiling and binning of NGS data (paragraph 3); 2. Materials and methods/2.2 Unix pipeline for assembly, taxonomic profiling and binning of NGS data (paragraph 5) Version: version of record | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Weights licence The inspected model-access documentation does not explicitly identify terms for this exact evaluated checkpoint or fitted head; repository code terms are shown separately. Individual claims | Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types 1. Introduction (paragraph 4); 4. Discussion (paragraph 1) Version: version of record | unreported automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Biological inputs NGS libraries from host-associated or environmental samples Individual claims | Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types Abstract (paragraph 1); 3. Results/3.3 Novel virome sequences from mink faecal samples (paragraph 1) Version: version of record | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Outputs Assembled contigs and taxonomic/viral profiles Individual claims | Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types 1. Introduction (paragraph 6); 3. Results/3.1 Excellent recall and precision for both simulated and real datasets (paragraph 3) Version: version of record | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Parameters Not applicable to a neural parameter count: this pipeline assembles, aligns and bins reads/contigs. Individual claims | Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types 2. Materials and methods/2.2 Unix pipeline for assembly, taxonomic profiling and binning of NGS data (paragraph 4); 2. Materials and methods/2.2 Unix pipeline for assembly, taxonomic profiling and binning of NGS data (paragraph 8) Version: version of record | inapplicable automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Known versions / configuration Lazypipe-nt is the comparison-table label; that label does not specify an immutable weight revision. Individual claims | Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types Model identification in the comparison table and corresponding Methods; immutable checkpoint revision is not supplied by the table label. Version: version of record | unreported automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
View linked audit checks and correction history
Release 2026-09-29-06401fd5b220 · Record review: needs review
1 source records and release history
- Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types · Original source · version of record
Technical metadata and extraction receipts
Stable ID: reported-model-8cb3dd4e9f5b10
- areas
- microbes-communities
- entity level
- method
- version
- Not reported
- reported name
- Lazypipe-nt
- historical missing metadata
- version: not_reported_in_legacy_extract; checkpoint revision: not_reported_in_legacy_extract; training data: not_reported_in_legacy_extract; licence: not_reported_in_legacy_extract
- metadata review scope
- historical_missing_metadata preserves the original discovery state. Current descriptive evidence and missingness are recorded in profile.facts; numerical-result review is separate.
- legacy kinds
- model
- entity classification
- review date: 2026-09-17; rationale: This record identifies a composed analysis workflow with separately identifiable upstream models, representations or tools and a downstream prediction/scoring procedure. Results belong to that complete composition rather than to an upstream model alone.; source ids: lazypipe-2020; source locator: 2. Materials and methods/2.2 Unix pipeline for assembly, taxonomic profiling and binning of NGS data (paragraph 3); 2. Materials and methods/2.2 Unix pipeline for assembly, taxonomic profiling and binning of NGS data (paragraph 5) | 2. Materials and methods/2.2 Unix pipeline for assembly, taxonomic profiling and binning of NGS data (paragraph 1); Abstract (paragraph 1); ambiguities: This is the paper-specific pipeline identity; unspecified component checkpoints or implementation versions are not inferred from its name.