At present, runBNG offers 12 mainly used functions in Bionano analyses, which are
------------------------------------------------------------------------------------------------------
Program: runBNG
Version: 2.0.1
Author: Yuxuan Yuan (yuxuan.yuan@outlook.com)
------------------------------------------------------------------------------------------------------
Synopsis: This pipeline aims to help complete key Bionano optical mapping analyses using command line
Usage: runBNG <command> [options]
Command: fa2cmap convert a given fasta format file into a cmap file
cmapstats check stats of a cmap file
bnxmerge merge different bnx files into one
bnxstats check stats of a bnx file
bnxfilter filter a bnx file
MQR get a molecule quality report for the Bionano data
repeatCheck check repeats using Bionano raw data
denovo de novo assemble Bionano single molecule maps
compare compare two different cmap files
hybrid perform Bionano hybrid scaffolding using one enzyme
dual perform Bionano hybrid scaffolding using two enzymes
SV structural variation detection
options: -h/-help show this message and exit
-----------------------------------------------------------------------------------------------------
•Ubuntu LTS or CentOS 6.4 or above or other equivalent Linux system •python v2.7.5 or greater •R v3.x •perl v5.10.x, v5.14.x or v5.16.x •gcc 4.4.7 or greater •glibc 2.15 or greater
Please download the latest Bionano Solve (Linux version). To determine which accelerator type should be used when selecting BioNano tools, please use the command "grep avx /proc/cpuinfo" or "grep sse2 /proc/cpuinfo" and search for the word ‘avx’ or ‘sse2’. If both types exist, use AVX as it is faster than SSE2.
BioNano Sovle (containing Bionano Pipeline and RefAligner/Assembler) needed by runBNG version 2 and above can be downloaded at: https://bionanogenomics.com/support/software-downloads For the Bionano packages requested by the old runBNG (version 1.3 and below), you may download the pacakges at: http://doi.org/10.5281/zenodo.4661675
dateutil
, lxml
data.table
, igraph
, intervals
and argparser
After all required dependencies are set, you can use 'runBNG' to start your analyses.
A manual detailing how to set and use 'runBNG' has been provided in the Manual.
We have also supplied a testing dataset (Examples). You may use this dataset to test this software.
Any problem in using 'runBNG' can be raised in the Issues.
Yuxuan Yuan, Philipp E. Bayer, HueyTyng Lee, David Edwards; runBNG: A software package for BioNano genomic analysis on the command line. Bioinformatics 2017 btx366. doi: 10.1093/bioinformatics/btx366
Thanks for using 'runBNG'!