preston/pfastqcount

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2
Language
C
License
MIT License
Created over 9 years ago
Updated over 9 years ago

preston/pfastqcount

preston

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pfastqcount is an optimized C implementation of a FASTQ sequence prefix counter. The program counts the number of times every four-nucleotide prefix is encountered via the sequential memory mapping of each ASCII-encoded FASTQ file into the process space. This is useful as part of a genomic data sequencing pipeline to sanity check that barcodes used in multiplexed sample experiments occur as expected. An alternative Ruby implementation is provided (pfastqcount.rb) for maximum portability and validation. The C implementation has been written for 64-bit Unix-like systems only. The output of the program is valid comma-separated value (CSV) data that may be opened in your favorite spreadsheet software such as Excel, OpenOffice, R etc.

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