The Padena algorithm supports FASTQ assembly (insofar as it needs only bases and makes no use of quality values) but it seems that PadenaUtil does not. We do have a parser for FASTQ.
Id #14114 | Release:
| Updated: Feb 13 at 8:43 PM by sjmercer | Created: Aug 17, 2011 at 9:46 PM by Rickbe
When calling QualitativeSequence.GetSubSequence(), the new QualitativeSequence object being returned does not retain the original information stored in the properties ID and metadata.
Id #13978 | Release:
| Updated: Feb 13 at 8:43 PM by reach2raziq | Created: Jul 22, 2011 at 11:55 PM by kch
verify that the results of a NUCmer alignment are correct. Do a multiple alignment on 4 sequences. You will receive 3 actual alignment objects containing an AlignedSequence object and a list of t...
Id #13633 | Release:
| Updated: Feb 13 at 8:43 PM by dourada | Created: Jun 2, 2011 at 2:48 AM by dourada
Self-contained archive containing solution and data to reproduce this bug can be downloaded at
When parsing a “/note” qua...
Id #13552 | Release:
| Updated: Feb 13 at 8:43 PM by FadiF | Created: May 21, 2011 at 12:58 AM by lbuckingham
I have a couple of issues I would like to discuss ( I am not sure if these are bug or unfinished items - a roadmap of your progress in this regards will be useful). Sorry for the long d...
Id #13534 | Release:
| Updated: Feb 13 at 8:43 PM by FadiF | Created: May 18, 2011 at 6:58 PM by KPonCodeplex2011
Applied biosystems DNA sequence format file contains a dna sequence in addition to a set of metadata associated with that sequence identify the chromatogram information that was used to determine t...
Id #13506 | Release:
| Updated: Feb 13 at 8:43 PM by labchef | Created: May 15, 2011 at 8:07 PM by jkolpak
I have developed some code using MBF framework 1.0 (which uses MBF.dll) for sequence analysis. I just downloaded beta version of the 2.0 framework (which uses Bio.dll). To my amazement, my projec...
Id #13443 | Release:
| Updated: Feb 13 at 8:43 PM by zyskowski | Created: Apr 30, 2011 at 12:03 AM by KPonCodeplex2011
create commandline utility that will convert from one file format to another file format.
Id #13218 | Release:
| Updated: Feb 13 at 8:43 PM by beatriza | Created: Mar 22, 2011 at 2:36 PM by dourada
NOTE: Reported by dourada
I was able to get #1 working. There was a problem reading the app.config file for Color data. I'm still not entirely sure what the real problem was, there are article...
Id #12925 | Release:
| Updated: Feb 13 at 8:43 PM by zyskowski | Created: Jan 28, 2011 at 12:18 AM by zyskowski
I downloaded the 2.0 preview source code, compiled it, and have a few questions:
The contents of the directory SourceSamples\ReadGenerator are empty
Thanks so much for your help a...
Id #12924 | Release:
| Updated: Feb 13 at 8:43 PM by zyskowski | Created: Jan 28, 2011 at 12:16 AM by zyskowski