I have run Velvet and ABySS using default parameters on my pair-end and single-end datasets, I have two questions related to the generated contigs. 1. …

Why Velvet and ABySS, the de Bruijn graph assemblers produce greater number of contigs than any other assembler? Ideally, a good assembler should generate less …

What is the difference between Exome sequencing versus RNA sequencing ? What type of de novo assemblers should be use for exome sequencing reads and …

Trying to index fastq reads but getting error Already preprocess fastq file using sga preprocess READS > out.fastq command. > sga index datafastq/humanUpairedSGA.fastq Building index …

<p>What is N50 in de novo genome assembler &quot;Velvet&quot;? and why we calculate it?</p>

There are numerous de novo assemblers such as ABySS, SPAdes, AMOS, etc. And there is only one transcript assembler that I know of: **Inchworm** in …

<p>Hi There,</p> <p>Recently I have been trying to improve a genome assembly. It is a plant genome. It was first assembled using 454 data. And …

<p>I was recently tasked by my lab to assemble a genome estimated at 850,000,000 bp. This is de novo and I've only had experience with …

<p>Is there a reference assembler (an assembler that uses a reference genome to base the assembly on) that will take multiple reference sequences? I have …

<p>Assuming contaminants are introduced into my sample (some of my skin sloughs off or whatever) and I use RNA-Seq to sequence my samples, if I …