HiLine

HiC alignment and classification pipeline.

Bioconda

HiLine is available on bioconda

conda install hiline

As a Command Line Program

HiLine --help

As a Python Class

from HiLine import Pipeline
help(Pipeline)

Requirments, Running

• Unix OS (MacOS / Linux)
• Python version 3.8 or later
• At least one of
  • bwa-mem2 version 2.0 or later
  • bwa version 0.7.17 or later
  • minimap2 version 2.17-r941 or later
    • gawk version 5.1.0 or later (if using minimap2)
    • perl version 5.30.3 or later (if using minimap2)
• Samtools version 1.10 or later

Requirments, Installing

• Python version 3.8 or later
• Pip
• Setuptools
• NumPy version 1.18.1 or later
• C/C++ compiler (tested with Clang version 9 and GCC version 7.3)
  
• Git
• Ninja
• Hyperscan build requirements
  • CMake
  • Boost version 1.61 or later
  • Ragel
  • PCRE
  • pkg-config

cd HiLine
pip install .
HiLine --help
python -c 'import HiLine'

Notes

• bwa-mem2 is the default mapper used by HiLine and is recommended over bwa, sans technical restrictions e.g. memory usage.
• By default, HiLine performs a 'read-trimming' step as part of the alignment process. A restriction enzyme-digested version of the reference genome is created, with filled-in blunt (biotin) ends. Reads are first mapped to the digested reference, portions of reads that align past the end of a restriction fragment (not including the blunt ends) are trimmed away. Trimmed reads are then aligned to the original reference. Trimming results in more accurate alignments, but halves the overall speed of the alignment process. Turn off read-trimming with the '--no-trim' options.
• Minimap2 alignments are processed through a script from the Arima Genomics mapping pipeline to select for 5' mappings, which filters out all other chimeric supplementary alignments. Such alignments, therefore, will not be available for output. Minimap2 mode is only recommended for quick, approximate mappings.

Third-Party Acknowledgements

HiLine uses the following third-party software and libraries

• Software
  • bwa-mem2
  • bwa
  • minimap2
  • Samtools
• Libraries
  • C/C++
    • Hyperscan
    • stb_sprintf.h
  • Python
    • Click
    • Pandas
    • NumPy
    • Seaborn
    • Matplotlib
    • Biopython
  • Perl
    • filter_five_end.pl