The development of the Genomic Next-generation Universal MAPper (GNUMAP) was performed at Brigham
Young University's Computational Sciences Laboratory under the direction of Dr. Mark Clement and
Dr. Quinn Snell from the Computer Science Department and Dr. Evan Johnson from the Statistics
- October 28, 2011: Version 3.0.2 Introduction of -k flag (to control number of matches)
Also, will print out same fastq scores as existed in input file.
- July 25, 2011: Version 2.9.0 Some stability fixes. Also included code for memory
- June 3, 2011: sam2sgr Version 2.0 Uses threading via openmp
- May 23, 2011: Version 2.6.0 Several stability updates included, in addition to significant
changes in bisulfite mapping. Including backward compatability so scripts will
perform the same way.
- February 22, 2011: Version 2.2.4 Introduced --print_all_sam flag in addition to XP and X0 flags
- December 13, 2010: Fixed SAM MAPQ characters (30 is good match, 0 is very poor)
- November 29, 2010: Ambiguity characters allowed in fasta reads
- November 09, 2010: sam2consensus program added
- November 06, 2010: Bisulfite .sgrex printing
- October 28, 2010: Version 2.2.1 Fixed error with catastrophic cancellation in PHMM
code. Algorithm is more stable with long sequences.
- October 20, 2010: Version 2.2.0 Update to alignment matrices. Much greater accuracy
on real data.
- September 20, 2010: Update to SNP calling for larger read totals. Using ratio instead
of pvalues for comparison
- August 30, 2010: Updates to output and SNP calling. Included ratio requirement for
diploid SNP calling.
- August 03, 2010: Version 2.1.7 Changed what FAST mode does. Also bug fixes and time
- July 22, 2010: Version 2.1.6 Fixes to Bisulfite mapping output. Also added SAM to SGR
converter, Version 1.0
- July 13, 2010: Version 2.1.5 Fixed memory leak, added
the --read_quality parameter. Working on MPI speedup.
- May 19, 2010: Version 2.1.0 Disallowed program from searching for
the same string multiple times. About 2x speedup.
- May 13, 2010: Version 2.0.1 Fixed MPI bugs and SAM output
- May 07, 2010: Version 2.0.0 Added MPI for both large memory machines (genome spread
across nodes) and small memory machines (reads spread across nodes)
- March 29, 2010: Version 1.5.75 Fixed a memory leak that was introduced in a previous version
- February 23, 2010: Version 1.5.6 Sam output and a larger genome capability
- February 17, 2010: Version 1.5.5 Added SAM output flag
- February 03, 2010: Version 1.5.3 Minor changes to improve speed
- January 11, 2010: Version 1.5 Fixed several bugs (including fastq sequence files and
SNP output in the .sgrex output file)
- December 29, 2009: Version 1.4.9 Fixed several bugs (including fasta sequence files),
only reads in a section of the sequences intead of all at once
- December 14, 2009: Version 1.4.8 Fixed the number of sequences report
- December 01, 2009: Version 1.4.7 Can read fasta sequences that are multi-lined
- December 01, 2009: Version 1.4.5 and 1.4.6 Bug fixes
- November 14, 2009: Version 1.4.0 Added functionality to read in both fastq and
fasta files (in addition to prb and int files).
- November 09, 2009: Version 1.3.3 Added examples/ directory
- November 05, 2009: Version 1.3.2 Bug fixes. Added --snp param.
- October 15, 2009: Version 1.3. Reduced memory footprint, added things to increase
speed. Will also print out each base when needed for the .sgrex file
- September 17, 2009: Version 1.2. Introduced flags for reading and writing of the
genome (reduced hashing and storing the genome to just under 5 minutes).
Also included a "sliding window" method to find a greater number of matches to
- July 27, 2009: Version 1.02.1. Bug fixes and optimization. Introduction of the
- 02 July, 2009: Version 1.01. Additional performance-enhancing modifications. Also
some bug fixes for reading in multiple genomes.
- 15 June, 2009: Version 1.0. Several modifications to create increased performance.
- 05 May, 2009: Version 0.99_5. Added -0 flag to print output at every position for
unequally lengthed sequences. Also included two other flags (-b and -d) to provide output for
assorted methylation analyses.
- 01 May, 2009: Version 0.99_4. Fixed an error with reading multiple chromosomes. Also
allowed for multiple chromosomes to be included in one file.
- 01 April, 2009: Version 0.99_3. Fixed an error with overflowing the size of a 32-bit
unsigned int. Using 64-bit unsigned long instead. Must compile under 64-bit mode (included in
- 10 February, 2009: Version 0.99_2 removed the SEQ_LENGTH variable so the sequences can have variable
lengths. Also allowed for the receipt for the adaptor sequence, removing any adaptor characters
especially for shorter sequences.
- Version 0.99 (02 Feb release) removed the popt library, using built-in command line parsing
- Version 0.99 of gnumap was released on January 07, 2009, with optimized alignment
- On December 30, 2008, the algorithm was updated, allowing a command-line argument for the
specification of a matrix identifying match and mismatch scores.
- August 20, 2008: Version 0.96 was released, allowing the user to include the analysis for many sequence files.
- On August 05, 2008, Version 0.95 was released, providing compatibility with both the _prb.txt
and _int.txt files.
- Version 0.9 (BETA) of gnumap was released on July 31, 2008 with full functionality.
Multithreading support was included to improve performance. The datagen program, used
to generate synthetic reads for duplicate analysis, was also included.
- Version 0.5 of gnumap was released on June 2, 2008 with limited functionality.
Synthetic benchmark datasets were also developed to measure the impact of duplicate reads on the
accuracy of different read mapping programs.
- At our research meeting on April 23, 2008, we developed the hashing algorithm. Most
mapping programs hash the reads and then make one pass across the genome to map the reads. In
order to account for duplicate reads, we decided that gnumap would need to hash the genome and
then map each read into muliple locations.
- On March 21, 2008, the architecture of gnumap was developed with a focus on statistical
methods to account for duplicate reads.
- Januray 11, 2008: Initial work on gnumap began when Dr Evan Johnson and his statistics
research group began meeting with researchers in the
Computational Sciences Laboratory.
This page last modified Wednesday May 21, 2014