BM-Map

A Powerful Bioinformatics Software Tool for Refining Next-Generation Sequencing (NGS) Read Mapping

Site Map

Home
News archive
Getting started
Manual
Download
Credits & Contacts

Latest Release

BM-Map 2.0.1

12/01/2011

For citation information, please go to Credits.

Related Tools

Publications

Ji, Y, Xu, Y, Zhang, Q, Tsui, K-W, Yuan, Y, Liang, S, Norris, C, Liang, H. BM-Map: Bayesian Mapping of Multireads for Next-Generation Sequencing Data. Biometrics.2011 Dec;67(4):1215-24. [PDF Full Text][Supplementary Info]

Authors

Yuan Yuan
Clift Norris
Yanxun Xu
Kam-Wah Tsui
Yuan Ji*
Han Liang*

Links

News Archive

Version 2.0.1 release - 12/01/2011
- Cross-platform Graphical User Interface (GUI) for BM-Map. This provides alternative solution for users who prefer graphical operation. The simple while informative graphical interface is straightforward and self-explanatory: just enter the user-defined parameters or choose from the pre-defined dropdown list and click "Go" button to run BM_Map. For backward compatibility, users can also use the command line to run BM-Map.
- Pre-built executable for certain Mac/Linux version . No need to make, just directly run from the command line or the GUI (tested on Snow Leopard and Ubuntu 10.04). For users who would like to play around the code, BM-Map source code is also supplied.
Version 2.0.0 release - 11/01/2011
- Now BM-Map accepts SAM, the most popular next-generation sequencing file format, as standard input. This means that the mapping results produced by many prominent mapping software packages can be readily used as the input file for downstream analysis performed by BM-Map. Since there are various ways of expressing mismatch information in SAM files, we strongly recommed using the Bowtie-produced SAM as input, which has been extensively tested for this version of BM-Map.
- Standardized output in SAM-like format. It retains all the required fields and information in original input SAM by appending the newly-calculated probability to the end of each line.
Version 1.0.5 release - 08/01/2011
- Added flanking feature. This provides more flexibility for calculating prior probability by considering the expression level in flanking regions of competing loci.
- Added strandness feature. Depending on the sequencing platform, some RNA-seq data may retain the original DNA stand information (+/-). Our BM-Map software is carefully designed to accommodate this situation when neccessary.
- Provided option for calculating proportional probability, Bayesian probability, or both. The program user can choose one of the following:
  1. Output the less accurate Proportional Probability : less time-consuming.
  2. Output the more accurate Bayesian Probability: 10-fold more time-consuming than calculating Proportional Probability alone.
  3. Output both Proportional Probability and the Bayesian Probability: takes same amount of time as calculating Bayesian Probability alone.
- Logged statistical and timing information during program execution. Previously, all information went to the console. Now we output important information to both the console and a log file so the user can monitor the current progress of BM-Map while keeping a disk copy of the program output.
Paper acceptance - 03/08/2011
- "BM-Map: Bayesian Mapping of Multireads for Next-Generation Sequencing Data" was accepted for publication in Biometrics.
Version 1.0.0 release - 11/19/2010
- Built Desktop version of BM-Map. Lots of optimizations were made to reduce the execution time and memory consumption, making BM-Map a desktop-runnable application.
- Added multi-thread feature. This largely improved the efficiency of BM-Map, taking full advantage of the power of modern multi-core CPU machines.
- Created "InputFile.txt" for specifying options in plain text file to replace the previous command-line option. With the ease of updating the contents in a text file, without the pain of memorizing the confusing command line options, BM-Map provided a user-friendly way of specifying user-defined input parameters.