Gap5 - new release (staden-2.0.0b6)

[jkbonfield]

I'm pleased to announce the latest version of the Staden Package, including Gap5, has been uploaded to SourceForge today. For those that are not aware of it, gap5 (and the predecessor gap4) are sequence assembly editing tools. Although gap5 also functions as a reasonable viewer, the primary goal is to produce an editor.

https://sourceforge.net/projects/staden/

This time there are prebuilt binaries for linux (x86_64 and i686 architectures) in addition to the usual source tarball. However note that these may not necessarily be compatible with all systems due to the huge variation between linux distributions.

Example data is included in the binary distributions within the example_data subdirectory, although it's not a huge short-read assembly for practical reasons.

James

PS. Some example screenshots:



The template display with the Y axis configured to sort by insert size. Clearly visible is a mixture of deep sequencing with short inserts and low coverage sequencing with larger inserts (capillary data in this case).




The contig editor with quality scales displayed in grey and differences between sequence and consensus shown in blue.

[aaross]

Is there a way to export a section of the contig with the consensus and all of the reads kept together? I would like to take a section of one Gap5 file and import it into another assembly with all of the reads intact.

Thanks,
Ash

[jkbonfield]

You should be able to export a region of a single contig as SAM or BAM, and then rerun tg_index on that SAM file to create a new assembly or append (tg_index -a -n) to an existing one.

Precisely what options are in the File->Export Sequences dialogue will depend on the version of Gap5 you have. (I really need to produce a new distribution as it's been too long.)

[aforntacc]

Hello all

Please this is my first time of using staden, my project seems simple, i have done sanger sequecning of some DNA fragments, i used the pregap4 to creat the data base and when i opened it in Gap4, it showed the contig.
Now my aim is to to verify the mutations, so i clicked the contig editor, i checked the cutoff, show reading quality in short i generally played around with various options including highlight disagreements then i clicked the trace diff option and i saw the overlapping peaks but when i clicked show mutation report an error pops up saying no reference specified.

please what are my doing wrong, i just want to compare the four ABI files WT_1_FRW.ABI WT_1_REV.ABI and MT_1_FRW.ABI, MT_1_REV.ABI.

Please and kindly assist me.

thank you