There is a long list of options/flags/parameters for a newbler assembly, some of which have been tre...
GenomicsRunning newbler: more de novo assembly parameters
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Genomics
BioinformaticsRunning newbler: de novo assembly
This post is about how to start up newbler for de novo assembly projects. I will describe setting up...
GenomicsNewbler output VI: the ‘status’ files
The files that are the topic of this post are all tables, i.e. tab separated text files. The ‘status...
GenomicsNewbler output V: the 454ContigScaffolds.txt and 454ScaffoldContigs.fna
In the post on what is new in newbler version 2.6, I introduced the -scaffold option. Briefly, with ...
GenomicsNewbler output IV: on ultra-short and single-read contigs
Sometimes you might observe very short contigs, some even having high read depth. You might see thes...
GenomicsNewbler output II: contigs and scaffolds sequence files, and the 454Scaffolds.txt file
The files most people are after when they do an assembly must be these: the actual contig and scaffo...
BioinformaticsNewbler output I: the 454NewblerMetrics.txt file
With this post, I’ll start going through the output files newbler generates. Some of these will be d...
TranscriptomicsRunning newbler: de novo transcriptome assembly I
Since version 2.3, newbler has a -cdna option for de novo transcriptome assembly. In this post, I’ll...
Genomicsnewbler输出结果文件454ContigGraph.txt内容介绍
The single file I’ll discuss today has in fact almost the entire assembly in it, besides the actual ...
GenomicsHow newbler works
I thought to start by explaining briefly how newbler works. I’ll do this by following the output new...