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TagDigger is a set of programs written in Python 3 that provide various utilities for genotyping-by-sequencing (GBS) and restriction site-associated DNA sequencing (RAD-seq) data. It is designed to use very little computer memory and be accessible to users lacking programming skill. Hopefully the Python functions written for TagDigger will also be useful to programmers working with GBS and RAD-seq data.

Available programs are:

• tagdigger_interactive.py: Read one or more FASTQ files and output a table of read counts for any user-specified set of barcodes and tags. Optionally, numeric genotypes (0, 1, 2) can also be output.
• tagdigger_script.py: Provides the same functionality as tagdigger_interactive.py, but in a non-interactive format such that it can be run from a bash script or batch file.
• barcode_splitter.py: Read one or more FASTQ files and a set of barcodes, and output new FASTQ files split by barcode, with barcode and adapter sequence removed. Optionally, output a table of MD5 checksums for each FASTQ file output. This program is intended to facilitate the deposit of data to NCBI/EBI/DDBJ for users who don't have access to Linux (or simply prefer that TagDigger interface to that of typical command-line software).
• barcode_splitter_script.py: A command-line version of barcode_splitter.py for running in a bash script or batch file.
• tag_manager.py: Identify matching tag sequences between different projects, and generate universal marker names across projects.
• exp_frag_size.py: For every tag or marker, determine the expected restriction digest fragment size by querying the reference genome.

An additional file, tagdigger_fun.py, contains functions used by the above programs, and is required for those programs to run.

The programs in TagDigger perform separate but related tasks. None of the programs necessarily needs to be run before any of the others (although output of tag_manager.py can be used as input for tagdigger_interactive.py or tagdigger_script.py).

For some tutorial information on TagDigger, see my lab meeting presentation.