Hi, I try to use Snap aligner (http://snap.cs.berkeley.edu/) and view the result in Igv for some viruses. Here is the Snap output: ![Snap output][1] After …

Hello, I understand that the suggested aligner to use with GATK is bwa. If I want to use Bowtie2 as the aligner, which reference file …

I want to know the tool that has the most support and is widely used. Are there any sequence alignment tool that works with Hadoop/HDFS …

Does anyone know a recent comparison done of the BWA-mem and Berkeley SNAP aligner? Especially if it leads to similar True Postive (TP), True Negative …

Has anyone else encountered an issue with setting two mismatches on bowtie2, using the `-N` flag (e.g., `-N 2`)? The error was: ``` Error: -N …

Is anyone still using [BWA][1] (Burrows-Wheeler Aligner) or have almost all switched to [Bowtie 2][2]? Our bioinformatics team has been evaluating both. BWA is quite …

Hello all, I am currently involved in a project where I have human blood and plasma samples, and I wish to examine the nonhuman DNA …

<p>Hi all,</p> <p>I just wonder why trinity and cufflink still use bowtie as defalut aligner to align reads back to the assembled transcripts? I went …

<p>I am trying to use <a href='http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml'>Bowtie2</a> for mapping reads to reference genome. I will use global alignment. I need to define the --score-min which …

<p>I am doing some experiment using <a href="http://bowtie-bio.sourceforge.net/index.shtml">BowTie</a> and <a href="http://alumni.cs.ucr.edu/~mvlachos/pubs/edbt2010.pdf">Q-Pick</a> which are short read aligners that aligns short DNA sequences (reads) to the human …