Bioinformaticians trying to assemble genomes or transcriptomes from large NGS libraries usually grap...
How do sequencing errors affect de Bruijn graphs?
Today’s commentary is the fourth in our de Bruijn graph series, but I did not like Roman characters ...
De Bruijn graphs(3)
In earlier commentaries, we introduced the concept of de Bruijn graphs and showed how they were used...
De Bruijn graphs(2)
In the previous post, we discussed how de Bruijn graphs can be constructed for a genome or a large s...
Algorithms for Next-gen Sequence Analysis
The field of next-gen sequence analysis is advancing so rapidly that new algorithms come out almost ...
Format of Velvet Output File ‘Roadmaps’
If you used Velvet genome assembler, you possibly have noticed a file named ‘Roadmaps’ being created...
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...
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...
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 ...
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...