Extracting contig info and singletons

fbarreto · 02-03-2010, 02:34 PM

Hi,

Our lab recently received 454 sequences back from Roche, and the files came in two types: all reads, and assemblies.
Should we have expected to also receive file(s) containing the singleton reads that didn't make it into the contigs? It seems to me such files would have been generated as a result of the assembly process, but we don't have them. We also don't have any info on the number of reads composing each contig.

Does anyone have any general insights or similar experiences?

Thanks!

maubp · 02-05-2010, 02:21 AM

Our local sequencing centers will generally us 454 data as the raw SFF file, plus the reads as FASTA with QUAL files (redundant if you can cope with the SFF file), plus a folder with all the output from running it through Newbler to give a draft assembly (redundant if you have the resources to run Newbler or other tools yourself). For example, the file 454ReadStatus.txt tells you which reads were used in contigs, were singletons, or were discarded.

Some sequencing centers will also generate some basic graphs, for example looking at the read lengths or contig lengths as a very simple way to gauge the overall quality/volume of output.

If you plan to do your own assembly or other analysis, I would ask for the raw SFF file.

02-03-2010, 02:34 PM	#1
fbarreto Junior Member Join Date: Jan 2010 Location: San Diego Posts: 5	Extracting contig info and singletons Hi, Our lab recently received 454 sequences back from Roche, and the files came in two types: all reads, and assemblies. Should we have expected to also receive file(s) containing the singleton reads that didn't make it into the contigs? It seems to me such files would have been generated as a result of the assembly process, but we don't have them. We also don't have any info on the number of reads composing each contig. Does anyone have any general insights or similar experiences? Thanks!

02-05-2010, 02:21 AM	#2
maubp Senior Member Join Date: Jul 2009 Location: Dundee, Scotland, UK Posts: 278	Our local sequencing centers will generally us 454 data as the raw SFF file, plus the reads as FASTA with QUAL files (redundant if you can cope with the SFF file), plus a folder with all the output from running it through Newbler to give a draft assembly (redundant if you have the resources to run Newbler or other tools yourself). For example, the file 454ReadStatus.txt tells you which reads were used in contigs, were singletons, or were discarded. Some sequencing centers will also generate some basic graphs, for example looking at the read lengths or contig lengths as a very simple way to gauge the overall quality/volume of output. If you plan to do your own assembly or other analysis, I would ask for the raw SFF file.