An assembly of reads, contigs and scaffolds

A blog on all things newbler and beyond

Posts Tagged ‘454Isotigs.txt’

Running newbler: de novo transcriptome assembly II: the output files

Posted by lexnederbragt on September 21, 2010

This post describes the transcriptome specific output files, or differencers between the files for transcriptome assembly relative to a regular assembly. For (aspects of) files not treated in this post have a look at these previous posts.

Alternative rope splicing (source: Wikimedia commons)

1) 454NewblerMetrics.txt
The differences for this file, relative to the same file for a ‘normal’ assembly (described in this post), are metrics on the isogroups and isotigs:

isogroupMetrics
{
numberOfIsogroups     = #####;
avgContigCnt          = #.#;
largestContigCnt      = ####;
numberWithOneContig   = #####;

avgIsotigCnt          = #.#;
largestIsotigCnt      = ##;
numberWithOneIsotig   = #####;
}

Besides the number of isogroups, the average and maximum number of contigs per isogroup are listed, as well as number of isogroups with only one contig. Below that, the average and maximum number of isotigs per isogroup are listed, as well as number of isogroups with one isotig. Read the rest of this entry »

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