This issue was created automatically by the metadata disambiguation pipeline because the associated block could not be resolved with high confidence.
Conflict Id: p:haphpipe/*
Conflict File: https://github.com/inab/research-software-etl/blob/pair_wise_cache/human_annotations/conflicts/p:haphpipe/*.json
Run Id: 20260205T170527Z-8c2d90e-test_9_0
A conflict has been detected between two software metadata entries with the same name but no shared repository or website. Please review the metadata and provide your decision using the format below.
Annotation Guidelines: refer to the annotation guidelines if needed.
Entry A - haphpipe
- Name: haphpipe
- ID: biotools/haphpipe/cmd/None
- Source: biotools
- Version: None
- Type: None
- Repository:
- Website:
- Authors:
- Publications: No publications listed.
- License: No license information.
- Documentation: No documentation available.
- Description:
Validation of Variant Assembly Using HAPHPIPE with Next-Generation Sequence Data from Viruses.
Next-generation sequencing (NGS) offers a powerful opportunity to identify low-abundance, intra-host viral sequence variants, yet the focus of many bioinformatic tools on consensus sequence construction has precluded a thorough analysis of intra-host diversity. To take full advantage of the resolution of NGS data, we developed HAplotype PHylodynamics PIPEline (HAPHPIPE), an open-source tool for the de novo and reference-based assembly of viral NGS data, with both consensus sequence assembly and a focus on the quantification of intra-host variation through haplotype reconstruction. We validate and compare the consensus sequence assembly methods of HAPHPIPE to those of two alternative software packages, HyDRA and Geneious, using simulated HIV and empirical HIV, HCV, and SARS-CoV-2 datasets. Our validation methods included read mapping, genetic distance, and genetic diversity metrics.
```
Entry B - haphpipe
- Name: haphpipe
- ID: bioconda_recipes/haphpipe/cmd/1.0.3,github/haphpipe/None/v1.0.3
- Source: github
- Version: None
- Type: None
- Repository:
- Website:
- Authors: No authors listed.
- Publications: No publications listed.
- License: No license information.
- Documentation:
- Description:
NGS viral assembly and population genetics.
HAplotype and PHylodynamics pipeline for viral assembly, population genetics, and phylodynamics.
Your Decision (in a code block below)
Use the exact format shown in a single comment, replacing the values as needed:
{
"decision": "same", // options: "same", "different", "unclear"
"explanation": "Brief explanation of your decision",
"confidence": "high" // options: "high", "medium", "low",
}
Thank you! Your annotation will be automatically ingested and logged.
A conflict has been detected between two software metadata entries with the same name but no shared repository or website. Please review the metadata and provide your decision using the format below.
Annotation Guidelines: refer to the annotation guidelines if needed.
Entry A - haphpipe
Next-generation sequencing (NGS) offers a powerful opportunity to identify low-abundance, intra-host viral sequence variants, yet the focus of many bioinformatic tools on consensus sequence construction has precluded a thorough analysis of intra-host diversity. To take full advantage of the resolution of NGS data, we developed HAplotype PHylodynamics PIPEline (HAPHPIPE), an open-source tool for the de novo and reference-based assembly of viral NGS data, with both consensus sequence assembly and a focus on the quantification of intra-host variation through haplotype reconstruction. We validate and compare the consensus sequence assembly methods of HAPHPIPE to those of two alternative software packages, HyDRA and Geneious, using simulated HIV and empirical HIV, HCV, and SARS-CoV-2 datasets. Our validation methods included read mapping, genetic distance, and genetic diversity metrics.
```
Entry B - haphpipe
Your Decision (in a code block below)
Use the exact format shown in a single comment, replacing the values as needed:
{ "decision": "same", // options: "same", "different", "unclear" "explanation": "Brief explanation of your decision", "confidence": "high" // options: "high", "medium", "low", }Thank you! Your annotation will be automatically ingested and logged.