protocols

Protocols for clinical analysis are in the wiki

---

Descriptions

Directories

(excluding submodules)

• NGS580: scripts used for NGS580 gene panel analysis
• bin_scripts: misc scripts and config files used to set up the bin directory (not included in repo) with installed software and packages needed for analysis
• cron: scripts and items used for automating tasks with cron
• demo: misc scripts used to demonstrate programming techniques for use elsewhere
• demultiplexing: scripts used for demultiplexing of NGS data
• generate-demultiplexing-reports: script & location for generation of demultiplexing reports for all runs in the NextSeq directory
• misc: scripts that don't fall into any other category
• reference-manuals: important user manuals needed for reference
• samplesheets: examle sample sheets used for analysis

Files

• bash_functions.sh: common set of functions used in various bash scripts
• bash_settings.sh: settings used by bash scripts
• example.email_recipients.txt: an example of what the email_recipients.txt file should look like for use in email scripts
• python_functions.py: common set of functions used in various Python scripts
• sequencer_settings.json: Select settings saved in JSON format for use with certain Python scripts
• settings: simple text file containing locations to scripts and directories, formatted for use with both Python and bash scripts
• template.py: template Python script

Submodules

• IGV-snapshot-automator: Use for making IGV snapshots
• demultiplexing-stats: Demultiplexing stats report for use with NextSeq
• run-monitor: (In development); Program for automatic monitoring of lab devices for processing of new data
• sh: Python module for easier access to system programs from within Python
• sns: NGS analysis pipeline customized for use on HPC cluster at NYUMC
• sns-wes-coverage-analysis: First-step analysis of coverage data output by sns pipeline
• sns-wes-downstream-analysis: Further post-processing of sns variant calling pipeline output
• toolbox: Utility scripts