An assembly of reads, contigs and scaffolds

A blog on all things newbler and beyond

Posts Tagged ‘454Scaffolds.txt’

Newbler output II: contigs and scaffolds sequence files, and the 454Scaffolds.txt file

Posted by lexnederbragt on March 22, 2010

The files most people are after when they do an assembly must be these: the actual contig and scaffold sequences. The contigs are in the files 454AllContigs and 454LargeContigs. ‘All’ indicates by default contigs of at least 100 bp, while ‘Large’ contigs are at least 500 bp. These lower limits can be set during assembly.
The ‘fna’ files contain the sequences (bases) in fasta format (I actually do not why this extension was chosen over ‘fasta’ or ‘fa’ which are most often used). The ‘qual’ files contain phred-like quality scores (see previous post). The contigs are in the same order between fna and qual files, and the quality scores are in the same order as the bases:

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