This code use used for analyzing High Throughput Sequencing (HTS) data, here referred to as Next-Gen Sequencing (NGS) data.

To run/use this code:

• python3 is required

• this requires the "Segment Processor" currently implemented as part of SPATS (on the segments branch), check it out:

$ git clone https://github.com/LucksLab/spats
$ git checkout segments

• set the NGS_HOME environment variable to point to the root of this repository

• set the SPATS_HOME environment variable to point to the root of the SPATS repository

• create a folder that holds the R1/R2 FASTQ files from the experiment

• configure your experiment: see the ngs_experiment2_keys() method in ngs/analysis.py for an example of how to specify the R1/R2 files for the experiment. in the current code, it expects the files to be named s1_full_r1.fastq, s1_full_r2.fastq, s2_full_r1.fastq, etc.

• execute analysis.sh in that same folder, e.g.,

$ $NGS_HOME/bin/analysis.sh

• similar setup/execution to NGS, but add "barcode":

$ $NGS_HOME/bin/analysis.sh barcode