Padenautil FASTQ support

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: None | Updated: Feb 13, 2013 at 8:43 PM by sjmercer | Created: Aug 17, 2011 at 9:46 PM by Rickbe

QualitativeSequence.GetSubSequence(): ID and metadata are not copied to the returned object

When calling QualitativeSequence.GetSubSequence(), the new QualitativeSequence object being returned does not retain the original information stored in the properties ID and metadata.   For exampl...

Id #13978 | Release: None | Updated: Feb 13, 2013 at 8:43 PM by reach2raziq | Created: Jul 22, 2011 at 11:55 PM by kch

verify NUCmer alignment results

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: None | Updated: Feb 13, 2013 at 8:43 PM by dourada | Created: Jun 2, 2011 at 2:48 AM by dourada

GenBank Parser: Incorrect parse when qualifier contains embedded '/' at start of a line.

Self-contained archive containing solution and data to reproduce this bug can be downloaded at http://bio.mquter.qut.edu.au/Downloads/GenBankParserBugReport.zip (5.5MB)   When parsing a “/note” qua...

Id #13552 | Release: None | Updated: Feb 13, 2013 at 8:43 PM by FadiF | Created: May 21, 2011 at 12:58 AM by lbuckingham

Getting original sequence names and IDs in aligned sequences

Greetings. 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: None | Updated: Feb 13, 2013 at 8:43 PM by FadiF | Created: May 18, 2011 at 6:58 PM by KPonCodeplex2011

Applied Biosystems Sequence Parser (abi, ab1)

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: None | Updated: Feb 13, 2013 at 8:43 PM by labchef | Created: May 15, 2011 at 8:07 PM by jkolpak

MBF framework 1.0 (MBF.dll) and MBF framework 2.0 (Bio.dll) are not compatible!

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: None | Updated: Feb 13, 2013 at 8:43 PM by zyskowski | Created: Apr 30, 2011 at 12:03 AM by KPonCodeplex2011

Create File Conversion commandline utility

create commandline utility that will convert from one file format to another file format.

Id #13218 | Release: None | Updated: Feb 13, 2013 at 8:43 PM by beatriza | Created: Mar 22, 2011 at 2:36 PM by dourada

Sequence Asesmbler: problem reading the app.config file for Color data

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: None | Updated: Feb 13, 2013 at 8:43 PM by zyskowski | Created: Jan 28, 2011 at 12:18 AM by zyskowski

The contents of the directory SourceSamples\ReadGenerator are empty

Greetings,   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: None | Updated: Feb 13, 2013 at 8:43 PM by zyskowski | Created: Jan 28, 2011 at 12:16 AM by zyskowski