Welcome to the EAGER Wiki¶
This is the main EAGER wiki, where all the information regarding installation, maintenance, updating and usage of the pipeline will be documented on several written wiki pages accompanied with tutorial material such as videos and short usage descriptions.
Contents:
- Prerequisites for the installation of EAGER
- Installation Instructions for the EAGER Pipeline
- General Usage of EAGER/EAGER-CLI
- Module description
- General Report Interpretation Guide
- Sample Number
- Sample name
- # of raw reads after C&M prior mapping
- # of merged reads
- # Reads not attempted to map
- % merged reads
- # mapped reads prior RMDup
- # mapped reads prior RMDup QF
- # of Duplicates removed
- Mapped Reads after RMDup
- Endogenous DNA (%)
- Cluster Factor
- Mean Coverage
- std. dev. Coverage
- Coverage >= 1X
- Coverage >= 2X
- Coverage >= 3X
- Coverage >= 4X
- Coverage >= 5X
- # SNPs
- AVG Coverage on mitochondrium
- Initial cont est
- Initial cont est low
- Initial cont est high
- Final cont est
- Final cont est low
- Final cont est high
- GC content
- # of reads on mitochondrium
- MT/NUC Ratio
- DMG 1st Base 3’
- DMG 2nd Base 3’
- DMG 1st Base 5’
- DMG 2nd Base 5’
- average fragment length
- median fragment length
- Tutorials
- FAQ
- I am missing Feature X for my analysis
- I have some BAM files already preprocessed and don’t want to map everything again
- I am using EAGER to reconstruct several genomes simultaneously but it doesn’t work
- I have several samples from the same individual (e.g. pre-screening and a wgs dataset) and would like to combine these
- I have an error and I don’t know what to do
- Licencing
- Citations