Mira3 Results After Assembly.

Question

[Walter]

After running the assembly successfully in mira3 I got the projectname_d_results directory having all the output files of assembly in different formats.

What I am interested in is the projectname_out.caf which can be further worked with by other tools.

I have already filtered the caf file and ready to be processed by other applications.

My question is what other tools can receive caf files as input and help me interpret the contig results.

Please also help me know how to download the Gap4 program from staden I have tried it but not through yet.

Answer 1

[User 59]

You already seem to know that gap4 is part of the Staden package, so it would seem sensible to download and install Staden first: http://staden.sourceforge.net/

gap5 is released however: http://seqanswers.com/forums/showthread.php?t=1923

I don't think gap4 reads caf natively, you will have to convert it to a gap4 compatible format

Answer 2

[Michael Schubert]

Mira has an executable called convert_project, which is able to convert to and from a variety of formats.

See

convert_project --help

for details.

For gap4, see the Staden package at Sourceforge.

Answer 3

[biobot 0.0.77.a.1099]

Starting with CAF format, you will need CAFTOOLS from the Sanger Institute FTP site. If you want to use gap4, CAFTOOLS includes caf2gap for this purpose. If you want to use gap5, the process has more steps; recent Staden packages include caf2baf to make BAF format. BAF format may be imported into gap5 via the tg_index program. In summary;

CAF -> caf2gap -> gap4

CAF -> caf2baf -> BAF -> tg_index -> gap5

I don't know whether mira3 produces padded or unpadded alignments. You may need to use caf_pad before loading into gap4 because gap4 requires padded alignments.