Reference health
Using prototyping to choose a bioinformatics workflow management system
17/17 checkable references clean · checked 2026-07-14
Every reference with a DOI in the deposited reference list resolved to a known work in Crossref or DataCite at the dated check, and none carried a publisher retraction, withdrawal, or removal notice.
19 without a DOI — not checked. A reference deposited without a DOI is never matched by title or guessed at; it stays outside the checked set, and this line discloses that.
The 17 checked references that resolve
resolves10.14806/ej.17.1.200
Cutadapt removes adapter sequences from high-throughput sequencing reads
resolves10.1093/bioinformatics/btq033
BEDTools: a flexible suite of utilities for comparing genomic features
resolves10.1101/gr.209601.116
UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy
resolves10.1093/nar/gky379
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update
resolves10.1093/nar/gkt328
The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud
resolves10.1038/s41587-020-0439-x
The nf-core framework for community-curated bioinformatics pipelines
The 19 references without a DOI — listed, not checked
no DOI — not checkedThe three technologies bioinformaticians need to be using right now
no DOI — not checkedA review of bioinformatic pipeline frameworks
no DOI — not checkedPlotkin JB, Shah P. riboviz: analysis and visualization of ribosome profiling datasets. BMC Bioinform
no DOI — not checkedCommon Workflow Language, v1.0. Specification
no DOI — not checkedOptions for RiboViz workflow management
no DOI — not checkedAwesome Pipeline
no DOI — not checkedComputational Data Analysis Workflow Systems
no DOI — not checkedDeveloping reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics
no DOI — not checkedGiven the experience of others writing bioinformatic pipelines, what are the pros/cons of Toil vs Snakemake vs Nextflow?
no DOI — not checkedWhich Bioinformatics Workflow Manager / Tool / Platform / Language / Specification / Standard do you use or prefer?
no DOI — not checkedFull-stack genomics pipelining with GATK4 + WDL + Cromwell [version 1; not peer reviewed]
no DOI — not checkedChoosing the right open-source software for your project
no DOI — not checkedCommon Workflow Language User Guide
no DOI — not checkedCollecting use cases for workflow level conditionals #725
no DOI — not checkedNextflow. Nextflow patterns. GitHub [Internet]. [cited 2020 Oct 19]. Available from: http://nextflow-io.github.io/patterns/index.html.
no DOI — not checkedNextflow tutorial
no DOI — not checkedsuggestion: run -dry #31
no DOI — not checkedriboviz: software for analysis and visualization of ribosome profiling datasets
no DOI — not checkedStreamlining Data-Intensive Biology With Workflow Systems
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