README.md

Graphical User Interface (Windows portable version)

A graphical user interface developped in Qt is available here (with GUI tutorial).

CLI (Linux)

Requirements

Please install the following modules & tools :

• python 2.7
• biopython
• tqdm
• samtools
• blastn & makeblastdb (>=2.3.0+)
• circos

Testing eKLIPse

python eKLIPse.py --test

add "-samtools", "-blastn", "-makeblastdb" and "-circos" options for executable files not in $PATH

Running eKLIPse

python eKLIPse.py -in <INPUT file path> -ref <GBK file path> [OPTIONS]

-in

The input file is a simple tabulated text file like:

path_bam1 <tab> title1

path_bam2 <tab> title2

-ref

eKLIPse accept any mtDNA reference genome in Genbank format.

rCRS (NC_012920.1.gb), CRS (J01415.2.gb) and Mus musculus (NC_005089.1.gb) are available in "/data"

[OPTIONS]

-out          <str>  : Output directory path                  [current]
-tmp          <str>  : Temporary directory path               [/tmp]
-scsize       <int>  : Soft-clipping minimal length           [25]
-mapsize      <int>  : Upstream mapping length                [20]
-downcov      <int>  : Downsampling reads number              [500000] (0=disable)
-minq         <int>  : Read quality threshold                 [20]
-shift        <int>  : Breakpoint BLAST shift length          [5]
-minblast     <int>  : Minimal number of BLAST per breakpoint [1]
-bilateral    <bool> : Filter non-bilateral BLAST deletions   [True]
-minMitoSize  <int>  : Filter resulting mitochondria size     [1000]
-id           <int>  : BLAST %identity threshold              [80]
-cov          <int>  : BLAST %coverage threshold              [70]
-gapopen      <int>  : BLAST cost to open a gap               [0:proton, 5:illumina]
-gapext       <int>  : BLAST cost to extend a gap             [2]
-thread       <int>  : Number of thread to use                [2]
-samtools     <str>  : samtools bin path                      [$PATH]
-blastn       <str>  : BLASTn bin path                        [$PATH]
-makeblastdb  <str>  : makeblastdb bin path                   [$PATH]
-circos       <str>  : circos bin path                        [$PATH]
--test               : eKLIPse test
--nocolor            : Disable output colors

eKLIPse outputs

• "eKLIPse_deletions.csv" containing all predicted deletions results
• "eKLIPse_genes.csv" summarizing cumulative deletion per mtDNA gene.
• circos plot representation for each input alignement. A example is shown below.

Contact

[email protected]

License

eKLIPse is available under the GNU Affero General Public License v3.0.

Please cite: .......