Documentation
The long versions: every option, every file, and how each decision is made. New to AMAP? Start here, then follow the tutorial.
Getting started
TutorialFrom an empty folder to a corrected genome, with the numbers of a real run.
InstallationNextflow, a container engine, and running without one.
QuickstartFrom an installed Nextflow to an open report.
Preparing inputsThe sample sheet, the genomes, and the checks run on them.
User guide
ParametersEvery option, its default, and when to change it.
Running AMAPProfiles, schedulers and larger runs.
OutputsEvery folder and file, and what a healthy run looks like.
The reportWhat each section of final_report.html shows.
The interactive reportamap_report.html, question by question, with or without eggNOG.
Custom referenceAny organism, against a trusted annotation of your own.
How it works
Step by step, illustratedOne gene at a time, from Bakta's call to what AMAP keeps.
OverviewWhat goes into a decision, and the five outcomes.
The workflowEach step of the pipeline, on the metro map.
The correction algorithmEvery rule and threshold, drawn on real genes.
Duplication metricsWhat the network numbers mean.
Deployment
ContainersThe AMAP image, what is in it, and building your own.
HPC clustersSchedulers, scratch, and where things should live.
TroubleshootingOrganised by the error you are looking at.