https://github.com/lpryszcz/hicembler

Assembler for HiC data
https://github.com/lpryszcz/hicembler

a-really-rubish-designer aseembly chromosomes genome hi-c scaffolding

Last synced: 15 days ago
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Assembler for HiC data

• Host: GitHub
• URL: https://github.com/lpryszcz/hicembler
• Owner: lpryszcz
• License: gpl-3.0
• Created: 2016-10-26T07:21:06.000Z (about 8 years ago)
• Default Branch: master
• Last Pushed: 2018-11-22T14:41:23.000Z (about 6 years ago)
• Last Synced: 2023-10-20T21:19:38.455Z (about 1 year ago)
• Topics: a-really-rubish-designer, aseembly, chromosomes, genome, hi-c, scaffolding
• Language: Python
• Size: 156 KB
• Stars: 4
• Watchers: 3
• Forks: 0
• Open Issues: 2
• Metadata Files:
  • Readme: README.rst
  • Changelog: CHANGELOG.md
  • License: LICENSE

Awesome Lists containing this project

README

        
.. contents:: Table of Contents

HiCembler

=========

This project was inspired by `DNA triangulation `_. 

============

Installation

============

On most Linux distros, the installation should be as easy as:

.. code-block:: bash

    sudo -H pip install -U matplotlib numpy scipy sklearn fastcluster pysam ete3 sinkhorn_knopp

    git clone --recursive https://github.com/lpryszcz/HiCembler.git

    cd HiCembler

    (cd bin/snap && make clean && make)

    (cd bin/idba && ./build.sh && ./configure && make)

Dependencies

~~~~~~~~~~~~

- Python dependencies: matplotlib, numpy, scipy, sklearn, fastcluster, pysam, ete3, `sinkhorn_knopp `_

- `SNAP aligner `_

- `IDBA `_ optionally

====================

Running the pipeline

====================

Parameters

~~~~~~~~~~

  -h, --help            show this help message and exit

  --version             show program's version number and exit

  -v, --verbose         verbose

  -i BAM, --bam BAM

                        BAM file(s)

  -f FASTA, --fasta FASTA

                        Genome FastA file

  -o OUTDIR, --outdir OUTDIR

                        output name

  -w WINDOWSIZE, --windowSize WINDOWSIZE

                        window size in kb used for scaffolding [[5, 10, 2]]

  -m MINSIZE, --minSize MINSIZE

                        minimum contig length [2000]

  -q MAPQ, --mapq MAPQ  mapping quality [10]

  -u UPTO, --upto UPTO  process up to this number of reads from each library [all]

  -t THREADS, --threads THREADS

                        number of processes to use [4]

  -d DPI, --dpi DPI     output images dpi [300]

  --minWindows MINWINDOWS

                        minimum number of windows per contig, has to be >1 [2]

Test run

~~~~~~~~

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Support

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Citation

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