HPSEQ - high-performance next-gen sequencing tools

Some fast tools for NGS data.

Available tools:

• hpcut - Simple adapter trimming based on Hamming distance.
• hpmerge - Simple paired-end read merging based on Hamming distance.
• hpscan_cw - like grep for (pairs of) FASTQ files (GNU fgrep actually).
• hpscan_sw - like the above but does full Smith-Waterman alignment

INSTALLATION

HPSEQ tools have build time dependencies on GNU grep, klib, and htslib. The dependencies can be downloaded and built if required using make deps.

HTSlib dependencies:

sudo apt-get install libz-dev
sudo apt-get install libbz2-dev
sudo apt-get install liblzma-dev

git clone "https://github.com/mcieslik-mctp/hpseq.git"
cd hpseq
make deps
make