An assembly of reads, contigs and scaffolds

A blog on all things newbler and beyond

Table of contents

Introduction
How newbler works

De novo assembly
Running newbler: de novo assembly

Running newbler: more de novo assembly parameters (and a hidden one)
Newbler output I: the 454NewblerMetrics.txt file

Newbler output II: contigs and scaffolds sequence files, and the 454Scaffolds.txt file
Newbler output III: the 454ContigGraph.txt file
Newbler output IV: on ultra-short and single-read contigs
Newbler output V: the 454ContigScaffolds.txt and 454ScaffoldContigs.fna
Newbler output VI: the ‘status’ files (454TrimStatus.txt, 454ReadStatus.txt, 454PairStatus.txt) and the 454AlignmentInfo.tsv file

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

Input to Newbler
Newbler input I: the sff file

Newbler input II: sequencing reads from other platforms
Newbler input III: a quick fix for the new Illumina fastq header

Scripts
A script for converting the 454NewblerMetrics.txt file to a tab-separated file

Miscellaneous
What is new in newbler 2.5.3
What is new in newbler 2.6

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