README.md

bgi2illumina

Conversion of BGI-sequenced headers of FASTQ records to Illumina-compatible ones.

Installation

Simply run make:

make          // this will build a binary
make install  // this will copy binary into /usr/local/bin

To delete existing "installation" run

make uninstall

Installation

Compilation process is very simple and can be handled without make, if you are more comfortable with it for some reasons.

Compile the source code with gcc:

gcc -o bgi2illumina bgi2illumina.c

or clang:

clang -o bgi2illumina bgi2illumina.c

Usage

./bgi2illumina <instrument>:<run_number>:<flowcell_id> < input.fq > output.fq

The support for gz-compressed files is provided through piping through bgzip -c and bgzip -cd (or gunzip -c).

BGI headers

BGI headers example:

@v300056266_run28L3C001R0010057888/1
@v300056266_run28L3C001R0010058124/1
@v300056266_run28L3C001R0010058591/1

It has the following structure:

{PREFIX}L{LANE}C{COLUMN}R{ROW}{TILE}/{READ}

In the example below:

PREFIX                  LANE   COLUMN   ROW  TILE      READ
@v300056266_run28     L 3    C 001    R 001  0057888 / 1
@v300056266_run28     L 3    C 001    R 001  0058124 / 1
@v300056266_run28     L 3    C 001    R 001  0058591 / 1

Contributing

Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.

Please make sure to update tests as appropriate.

License

MIT