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pairDistance - Programs for collect, analyze and visualization pair-ends reads distance.


Commands And Options
License And Citation


Here we describe the programs for collecting, analyzing and visualizing distances within paired-end reads. Pair_distance program attempts to align reads on contigs and collects statistical data on distance between reads. Then, a user can load that data into visualization program SView than select a region on a curve and get parameters of distribution.


To collect information about distance in paired-end reads.

./bin/pair_distance chr13.fa reads.fa -o:pd.cfg 

To display distribution chart of distances (Fig. 1).

./SView/Sview  -type PE

Fig. 1 Result of the visualization.

Commands And Options

./pair_distance contig.fna reads.fna -o:config [options], 


contig.fna - fasta file with one or more genomic contigs.

reads.fna - fasta file with paired-end reads, sequences of paired reads should be in order even/odd.

pair_distance options:

-PE_only - selects data for "PE" reads only
-MP_only - selects data for "MP" reads only
-DE_only - selects data for "distance ends" reads only with very long distances (>1K bp) between ends.

A name of an output file is the same as a name of input with added “.distance” extension.

./SView -type PE|MP|DE 

Sview is a QT-based GUI program for analysis and visualization of distance data on paired-end reads. User must specify type of paired reads before loading a data file.

-type PE|MP|DE - specifies reads type.

-in "data.bin" - loads file with data in binary format. Usr can also specify a datafile in menu "File"

-out "result.txt" - specifies name of an output file. If name isn’t specified, an output will be printed in stdout.

User can navigate a distribution curve with a mouse wheel and use Ctrl-mouse wheel to zoom in and out. Statistic data is printed in an info window if a representative part of curve is selected by clicking and dragging a mouse pointer. For "PE" and "DE" reads, user must select a single area. In case of “MP” reads, user can switch between types of area by pressing "PE" and "DE" buttons in a toolbar. User can save an output by pressing a button on a toolbar or by using "File>Save" menu command.

License And Citation

pairDistance is free for academic usage. For commercial licensing, please inquire to


pairDistance for academic usage can be downloaded here