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Assembler for HiC data
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array2scaffolds.py
bam2clusters.py
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test_clustering.py
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test_scaffolding.py

README.rst

HiCembler

This project was inspired by DNA triangulation.

Installation

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

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

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

Support

Citation

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