Version 2.0.6632.1

Released on February 27, 2025

Download at: https://download.jetbrains.com/biolabs/span/span-2.0.6632.jar

Changes:

• Improved integration with JBR - whole genome peak calling model parameters estimation
• Reworked fragmentation analysis and compensation, introduced --f-light, --f-hard and --f-speed parameters to compute fragmentation compensation gap

Version 2.0.6632

Released on February 27, 2025

Download at: https://download.jetbrains.com/biolabs/span/span-2.0.6632.jar

Changes:

• Improved integration with JBR - whole genome peak calling model parameters estimation
• Reworked fragmentation analysis and compensation, introduced --f-light, --f-hard and --f-speed
  parameters to compute fragmentation compensation gap

Version 2.0.6610

Released on January 20th, 2025

Download at: https://download.jetbrains.com/biolabs/span/span-2.0.6610.jar

Changes:

• Added --chromosomes parameter to limit analysis to selected chromosomes only
• Added --hmm-snr and --hmm-low parameters to tweak constraints during HMM fitting
  (defaults are optimized for a broad range of ChIP-seq experiments)
• Added --fragmentation and --gap-fragmentation parameters to configure compensation gap
  for tracks with high fragmentation
• Added --clip parameter to configure local signal clipping to refine peaks boundaries

Version 2.0.6558

Released on November 11th, 2024

Download at: https://download.jetbrains.com/biolabs/span/span-2.0.6558.jar

Changes:

• Improved performance in various signal-to-noise conditions with data-estimated constraints of signal-to-noise ratio and minimal noise state threshold
• Fixed aggressive signal upscaling in case of exceeding control library sizes
• Sensitivity and gap are computed automatically based on experimental data
• Support blacklisted regions --blacklist
• Support --deep-analysis additional analysis of peak calling producing important statistics
• Extended logging in debug mode --debug
• Configure multiple hypothesis adjustment method with --multiple

Version 1.6.6499

Released on April 30th, 2024

Download at: https://download.jetbrains.com/biolabs/span/span-1.6.6499.jar

Changes:

• Faster SPAN model convergence by relative likelihood estimation
• Improved initialization to make SPAN more robust in low signal-to-noise ratio case
• Don't process contigs when coverage distribution is different from genome-wise
• Introduced --bg-sensitivity to configure sensitivity of peak backgrounds
• Dropped gap as obsolete
• Peaks from model procedure significantly improved tuning flexibility

Version 1.5.6351

Released on Feb 2nd, 2024

Download at: https://download.jetbrains.com/biolabs/span/span-1.5.6351.jar

Changes:

• Specify log file location with --log command line option
• Don't keep cache files until --keep-cache parameter is provided

Version 1.4.6197

Released on November 2nd, 2023

Download at: https://download.jetbrains.com/biolabs/span/span-1.4.6197.jar

Changes:

Fixed problem with SPAN ignoring --threads command line argument

Version 1.3.5677

Released on July 20th, 2023

Download at: https://download.jetbrains.com/biolabs/span/span-1.3.5677.jar

Changes:

• Fixed problem with paired end coverage loading and too long paired fragments

Version 1.2.5668

Released on June 27th, 2023

Download at: https://download.jetbrains.com/biolabs/span/span-1.2.5668.jar

Changes:

• Improved peak calling for narrow marks histone marks
• Fixed beta value estimation for control correction on chromosome-filtered coverage
• Fixed problem with highly relaxed FDR settings

Version 1.1.5628

Released on March 9th, 2023

Download at: https://download.jetbrains.com/biolabs/span/span-1.1.5628.jar

Changes:

• Bugfix update - fix problem with treatment and control scaling
• Upscale treatment and control library
• Slightly tweaked defaults - number of iterations and threshold till convergence
• Reverted compatibility with Java 8