Welcome to split_library_log_parser’s documentation!

Author: Menachem Sklarz

Date: 24/1/2017

Why should I need this?

When using QIIME, one of the first steps is the split_libraries_fastq.py script which performs demultiplexing of Fastq sequence data where barcodes and sequences are contained in two separate fastq files, while also doing some basic quality testing.

This step creates a log file, split_library_log.txt, which contains statistics about the number of reads per sample that passed the various tests and manipulations.

parse_split_library_log.R converts this text file into a tsv table, which is more convenient for comparison between the samples etc.

Usage

Simple! Just execute the following::

Rscript parse_split_library_log.R   \
    --input split_library_log.txt   \
    --output split_library_log.tsv

Where:

--input file Path to split_library_log.txt
--output file Path to tab-delimited output file

Dependencies

Please make sure you have the following libraries installed in your R version:

  • magrittr
  • optparse
  • tools