gsAssembler (v2.6) - result files

[fungalE]

I recently received the data from the sequencing lab. ESTs were sequenced with 454 sequencer and assembled using gsAssembler (v2.6).

This is totally new area for me. Actually, I am not sure if I they gave me all the necessary result files.

Could you tell where from the result files I can find these data:

• number of high quality ESTS
• average length of quality sequence
• number of contigs
• number of singlets
• total number of unique sequences (unigenes?)
• number of ESTs assembled into contigs
• average G+C content of unigenes
• Total raw reads
• Total bases
• Reads after quality control and trimming
• Bases entering assembly
• Aligned reads
• Aligned bases
• Assembled reads
• Repeats
• Outliers
• Too short
• Total isogroups
• Average contig content
• Largest contig content
• Number with one contig
• Average isotig content
• Largest isotig content
• Number with one isotig
• Total isotigs
• Number of bases
• Average isotig size
• Largest isotig size
• Number of contigs
• Average contig size
• Largest contig size
• unassembled reads
• how many read/contigs
• how many % contigs contained 10 read or more
• how many were removed due to their length or because of their low quality score

Thanks a lot!

[sklages]

As a starting point you may have a look here, http://contig.wordpress.com/ , very good explanations. You could also ask your provider for information on assembly output.

[Jeremy]

I also recommend reading the manual for Newbler v2.6, you should have no problem finding a .pdf of it from a google search. It describes the input parameters and the output files and should give a pretty good idea of what everything is and where to find the information you need.

The problem with data sets this big is that the information you need is split up among several different files, so for some of the things you asked for you actually need to take a bit of information out of a few different files.

A lot of the assembly quality information is in '454NewblerMetrics.txt' and this is the very first file I look at every time I get a new lot of data.