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首页发表于2012年03月的文章
Running newbler: more de novo assembly parameters Genomics

Running 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
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Running newbler: de novo assembly Bioinformatics

Running 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
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Newbler output VI: the ‘status’ files Genomics

Newbler 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
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Newbler output V: the 454ContigScaffolds.txt and 454ScaffoldContigs.fna Genomics

Newbler 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
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Newbler output IV: on ultra-short and single-read contigs Genomics

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

Newbler 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
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Newbler output I: the 454NewblerMetrics.txt file Bioinformatics

Newbler 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
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Running newbler: de novo transcriptome assembly I Transcriptomics

Running 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
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newbler输出结果文件454ContigGraph.txt内容介绍 Genomics

newbler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
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How newbler works Genomics

How 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
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