Table of Contents
This project was inspired by DNA triangulation.
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)- Python dependencies: matplotlib, numpy, scipy, sklearn, fastcluster, pysam, ete3, sinkhorn_knopp
- SNAP aligner
- IDBA optionally
-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]