ReviewBriefings in bioinformatics2017
A review of bioinformatic pipeline frameworks.
Review in Briefings in bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 103 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
103 citing papers in PubMed.
- A scoping review of approaches to evaluating workflow management systems for bioinformatics users.Briefings in bioinformatics · 2026Article
- SNPio: a Python interface for population genomic data processing.BMC bioinformatics · 2026Article
- Responsible Use of Large Language Models in Microbial Genomics and Bioinformatics: A Life-Science Framework for Reliability, Reproducibility, and Risk-Aware Interpretation.Life (Basel, Switzerland) · 2026Review
- TaxaScope: a container-native, visualization-centric workstation for genome-based bacterial taxonomy.Frontiers in microbiology · 2026Article
- CBIcall: a configuration-driven framework for variant calling in large sequencing cohorts.Bioinformatics advances · 2026Article
- User-friendly scheduler Using a hybrid architecture and supercomputing for big data processing.bioRxiv : the preprint server for biology · 2025Article
- The Nextflow nf-core/metatdenovo pipeline for reproducible annotation of metatranscriptomes, and more.PeerJ · 2025Article
- eQTL-Detect: nextflow-based pipeline for eQTL detection in modular format with sharable and parallelizable scripts.NAR genomics and bioinformatics · 2024Article
- BioPipeline Creator-a user-friendly Java-based GUI for managing and customizing biological data pipelines.Scientific reports · 2024Article
- The GEA pipeline for characterizing Escherichia coli and Salmonella genomes.Scientific reports · 2024Article
- A Bioinformatics Toolkit for Next-Generation Sequencing in Clinical Oncology.Current issues in molecular biology · 2023Review
- Article
- The five pillars of computational reproducibility: bioinformatics and beyond.Briefings in bioinformatics · 2023Article
- SnakeLines: integrated set of computational pipelines for sequencing reads.Journal of integrative bioinformatics · 2023Article
- Integrative multi-omics and systems bioinformatics in translational neuroscience: A data mining perspective.Journal of pharmaceutical analysis · 2023Review
- polishCLR: A Nextflow Workflow for Polishing PacBio CLR Genome Assemblies.Genome biology and evolution · 2023Article
- MXP: Modular eXpandable framework for building bioinformatics Pipelines.Journal of bioinformatics and systems biology : Open access · 2023Article
- Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case.Wiley interdisciplinary reviews. Computational molecular science · 2022Article
- Whole Genome Sequencing Contributions and Challenges in Disease Reduction Focused on Malaria.Biology · 2022Review
- LPMX: a pure rootless composable container system.BMC bioinformatics · 2022Article
43 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-throughput bioinformatic analyses increasingly rely on pipeline frameworks to process sequence and metadata. Modern implementations of these frameworks differ on three key dimensions: using an implicit or explicit syntax, using a configuration, convention or class-based design paradigm and offering a command line or workbench interface. Here I survey and compare the design philosophies of several current pipeline frameworks. I provide practical recommendations based on analysis requirements and the user base.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.