Programs used to analyze data from Freq Seq
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FREQSeq
FreqSeqWPF
TestData
freqout
.gitattributes
.gitignore
AFSeq.sln.DotSettings.user
AF_BarCodes.txt
AddBarcode.py
CM1145_alleles.txt
CreateOptionsXML.py
Example.xml
ExampleCMD.sh
FghA Alignment.txt
FreqSeq.sln
FreqSeq.suo
FreqSeq.userprefs
FreqSeq.v11.suo
MakeXML.py
README.md
README_UBUNTU
SimpleExample.xml
build.sh
config

README.md

FreqSeq

Programs used to analyze data from Freq Seq Data. See the main documentation pages at:

http://www.evolvedmicrobe.com/FreqSeq/index.html

The source code is divided in to several folders.

  • FreqSeqWPF - the WPF client on windows
  • FreqSeq- The library file containing the methods used by the GUI and command line programs.
  • freqout - The command line program.

New Version on 9/27/2015

Bugs Fixed:

  • Warning message if unequal length alleles are input into the program.

Improvements:

  • Compiled binary version released for Ubuntu 14.04

New Version on 12/4/2013

Bugs Fixed:

  • Bug in Smith-waterman-Gotoh alignment (The +/- sign on the penalty for the gap creation and extension was switched, leading to incorrect alignments)
  • Bug in barcode assigner – barcodes within hamming distance of 1 were not being assigned.

Improvements:

  • Reads gzipped fastq files (ending with .gz)
  • Changed command line executable name to freqout
  • Trimmed long sequences to within only 10 bp longer than the expected read to improve alignment speed and accuracy
  • Increased hashing k-mer length to 9 to reduce the number of alignment candidates identified
  • Automatically skipping reads less than 75 bp (minimum length can be set in XML).
  • Output column names changed