Lynch Lab Pipeline Repository
Thank you for visiting this site! Below are the current versions of the analysis pipelines available from our group.
To sign up for office hours with Katie, please use this link.
To report an issue (bug, odd behavior) with any script, please fill out this form, and current status of your reported issue can be viewed here.
Current Documentation and Support Links
16S Processing (from raw files to ASVs), version 2.0
16S Data Analysis, version 2.0
ITS2 Processing Document (USEARCH)
ENA Sequence Read Archive Steps
Scripts are also available on wynton (/wynton/group/lynch/kmccauley/lab-code) and LynchServer2 (/data/Users/kmccauley/LabCode). Updates are made and transferred to both locations, so versions should be consistent. You can also visit github directly at: https://github.com/lynchlab-ucsf/lab-code
Example Mapping File
A de-identified example mapping file can be found here
Previous Pipeline Versions
Last updated on: 17 Dec 2021