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BioCDQA

A Retrieval-Augmented Knowledge Mining Method with Deep Thinking LLMs for Biomedical Research and Clinical Support

Introduction

Knowledge graphs and large language models (LLMs) serve as key tools for biomedical knowledge integration and reasoning, facilitating the structured organization of literature and the discovery of deep semantic relationships. However, existing methods still face challenges in knowledge mining and cross-document reasoning: knowledge graph construction is constrained ...

Type: Unrecognized workflow type

Creator: Yichun Feng

Submitter: Yichun Feng

DOI: 10.48546/workflowhub.workflow.1744.1

BioCDQA

A Retrieval-Augmented Knowledge Mining Method with Deep Thinking LLMs for Biomedical Research and Clinical Support

Introduction

Knowledge graphs and large language models (LLMs) serve as key tools for biomedical knowledge integration and reasoning, facilitating the structured organization of literature and the discovery of deep semantic relationships. However, existing methods still face challenges in knowledge mining and cross-document reasoning: knowledge graph construction is constrained ...

Type: Unrecognized workflow type

Creators: None

Submitter: Yichun Feng

nf-core/createtaxdb

GitHub Actions CI Status GitHub Actions Linting StatusAWS CI[![Cite ...

Type: Nextflow

Creators: None

Submitter: WorkflowHub Bot

vvv2_align_SE_minimap2_pacbio
Stable

Using:

  • vadr annotation (virus model must be selected in options)
  • vardict variant caller
  • coverage depth Provides summarizing files:
  • png image of variant calling with annotations and coverage depths
  • tsv file with all information of significant variants only

Type: Galaxy

Creators: Fabrice Touzain, This study was founded by the French National Research Agency and by Santé publique France as part of the project "EMERGEN". Anses Ploufragan research was also supported by Agglomération de Saint-Brieuc, Département des Côtes d'Armor and Région Bretagne

Submitter: Fabrice Touzain

VVV2_align_SE
Deprecated

SINGLE-END workflow. Align reads on fasta reference/assembly using bwa mem, get a consensus, variants, mutation explanations.

IMPORTANT:

  • For "bcftools call" consensus step, the --ploidy file is in "Données partagées" (Shared Data) and must be imported in your history to use the worflow by providing this file (tells bcftools to consider haploid variant calling).
  • SELECT the mot ADAPTED VADR MODEL for annotation (see vadr parameters).

Type: Galaxy

Creator: Fabrice Touzain

Submitter: Fabrice Touzain

VVV2_align_PE
Deprecated

PAIRED-END workflow. Align reads on fasta reference/assembly using bwa mem, get a consensus, variants, mutation explanations.

IMPORTANT:

  • For "bcftools call" consensus step, the --ploidy file is in "Données partagées" (Shared Data) and must be imported in your history to use the worflow by providing this file (tells bcftools to consider haploid variant calling).
  • SELECT THE MOST ADAPTED VADR MODEL for annotation (see vadr parameters).

Type: Galaxy

Creator: Fabrice Touzain

Submitter: Fabrice Touzain

vvv2_align_SE_bwamem2_nanopore
Stable

Using:

  • vadr annotation (virus model must be selected in options)
  • vardict variant caller
  • coverage depth Provides summarizing files:
  • png image of variant calling with annotations and coverage depths
  • tsv file with all information of significant variants only

Type: Galaxy

Creators: Fabrice Touzain, This study was founded by the French National Research Agency and by Santé publique France as part of the project "EMERGEN". Anses Ploufragan research was also supported by Agglomération de Saint-Brieuc, Département des Côtes d'Armor and Région Bretagne

Submitter: Fabrice Touzain

vvv2_align_PE_bwamem2
Stable

Using:

  • vadr annotation (virus model must be selected in options)
  • vardict variant caller
  • coverage depth Provides summarizing files:
  • png image of variant calling with annotations and coverage depths
  • tsv file with all information of significant variants only (can be opened in Excel/LibreOffice)

Type: Galaxy

Creators: Fabrice Touzain, This study was founded by the French National Research Agency and by Santé publique France as part of the project "EMERGEN". Anses Ploufragan research was also supported by Agglomération de Saint-Brieuc, Département des Côtes d'Armor and Région Bretagne

Submitter: Fabrice Touzain

vvv2_align_SE_bwamem2
Stable

Using:

  • vadr annotation (virus model must be selected in options)
  • vardict variant caller
  • coverage depth Provides summarizing files:
  • png image of variant calling with annotations and coverage depths
  • tsv file with all information of significant variants only (can be opened in Excel/LibreOffice)

Type: Galaxy

Creators: Fabrice Touzain, This study was founded by the French National Research Agency and by Santé publique France as part of the project "EMERGEN". Anses Ploufragan research was also supported by Agglomération de Saint-Brieuc, Département des Côtes d'Armor and Région Bretagne

Submitter: Fabrice Touzain

nf-core/metatdenovo

GitHub Actions CI Status GitHub Actions Linting StatusAWS CI[![Cite ...

Type: Nextflow

Creators: Danilo Di Leo, Emelie Nilsson & Daniel Lundin

Submitter: WorkflowHub Bot

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