An assembly of reads, contigs and scaffolds

A blog on all things newbler and beyond

Posts Tagged ‘paired end’

Newbler input III: a quick fix for the new Illumina fastq header

Posted by lexnederbragt on September 1, 2011

One unfortunate drawback of working with Illumina sequences is the many changes to the format of their fastq readfiles. The quality scoring has been changed several times since the first Solexa reads become available. It appears they have now settled on the Sanger style, see this wikipedia entry.

(Source: thepoolandspashoponline.com.au)

Regrettably, with their latest software upgrade (Casava 1.8), the headers (sequence identifiers) in the fastq files have changed. The change is described in the aforementioned wikipedia entry; basically, some elements have been added, some have changed order, and there are now two parts seperated by a space.

I wouldn’t have written this blogpost if this change had not been relevant for newbler: we were lucky enough to enjoy direct reading of Illumina fastq files (with newbler determining the quality scoring type) starting with newbler 2.6. newbler also matches mate-pairs (Illumina read 1 and read 2), so that these can be used as paired-ends by newbler (to build scaffolds). By the way, FASTQ files from the NCBI/EBI Sequence Read Archive are also correctly parsed for mate pairs, but here the filename is used for determining read 1 and read 2.

Read the rest of this entry »

Posted in Newbler input | Tagged: , , , | 5 Comments »

Newbler input II: sequencing reads from other platforms

Posted by lexnederbragt on January 21, 2011

A sanger sequence read electropherogram (source: wikipedia)

Both the runMapping and runAssembly programs are able to take in reads from other platforms, at least Sanger reads and Illumina reads. As long as the reads are in fasta format, with an optional quality file, newbler accepts and uses these reads. When the fasta files contain paired end (mate pair) reads, newbler can actually be made to use the pair information.

In general, it is a good idea to clean your fasta sequences before adding them to newbler: remove vectors, linkers, low quality parts of reads, or entire low quality reads first.
Also note that, while for sff files a symbolic link is generated in the assembly or project folder (still present after the program is finished when the -nrm flag is set), fasta files are not included in this way.

Read the rest of this entry »

Posted in Newbler input | Tagged: , , , , , | 20 Comments »