GenomicsRunning newbler: more de novo assembly parameters There is a long list of options/flags/parameters for a newbler assembly, some of which have been tre... 03月31日 1,408 评论 阅读全文
BioinformaticsRunning newbler: de novo assembly This post is about how to start up newbler for de novo assembly projects. I will describe setting up... 03月31日 2,115 评论 阅读全文
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... 03月31日 462 评论 阅读全文
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 ... 03月31日 427 评论 阅读全文
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... 03月31日 553 评论 阅读全文
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... 03月30日 898 评论 阅读全文
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... 03月30日 471 评论 阅读全文
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... 03月30日 1,252 1 阅读全文
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 ... 03月30日 767 评论 阅读全文
GenomicsHow newbler works I thought to start by explaining briefly how newbler works. I’ll do this by following the output new... 03月30日 1,290 1 阅读全文