FASTQ compression via boosting Sequence Compression Algorithms using Locally Consistent Encoding
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Makefile
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arithmetic.cpp
arithmetic.h
buffio.cpp
buffio.h
compress.cpp
compress.h
const.cpp
const.h
decompress.cpp
decompress.h
main.cpp
names.cpp
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patterns.bin
qualities.cpp
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README.md

SCALCE - Sequence Compression Algorithms using Locally Consistent Encoding

How to install?

In most cases, typing

git clone https://github.com/sfu-compbio/scalce.git
cd scalce
make download
make

should result in a happy scalce executable. make download will download all necessary dependencies necessary for building SCALCE.

We also recommend that you install pigz and make the pigz executable reachable via PATH variable.

If this doesn't work, please open a Github issue and we'll try to sort it out.

Warning

Variable-length reads (e.g. Pacbio) are not fully supported! There is a limited support (described in documentation); however, it is not tested and is rather buggy. Use caution and make sure to test decompression validity on Pacbio reads!

More stuff...

... is available at http://sfu-compbio.github.io/scalce/.