This is an old revision of the document!
This page is currently under construction.
As a first introduction into NGS alignment software tools we recommend reading this short blog post. Or in other words: It might be, that the list of supported tools grows and grows, due to your requests, but will never really cover everybody's favorite tool.
BWA is one mapping tool, particularly to map “low-divergent sequences against a large reference genome”. Modules on Mogon can be found as1):
The wrapper script is not installed, yet.
To leverage the task from 1 (or a few) samples to be mapped to several in parallel, we provide a wrapper script, which is available as a module:
The code is under version management and hosted internally, here.
The wrapper script will submit a job, it is not intended to be just within a SLURM environment, but rather creates one.
parallel_BWA -h will display a help message with all the options, the script provides. Likewise, the call
parallel_BWA –credits will display credits and a version history.
The script, after loading the module, can then be run like:
$ parallel_BWA [options] <referencedir> <inputdir>
*.fastq” or “
*.fq” and will allways assume FASTQ files (compressed or uncompressed).
_1” and “
_2” or “
_R1” and “
bwa memand only sets up a few things to yield performance.
referencedirneeds to be the (relative) path to a directory containing an indexed BWA reference
inputdirneeds to be a (relative) path to a directory containing all inputs. Subdirectories and files containing the string
unpairedare ignored; this is to support preprocessing with the trimmomatic module.
parallel_BWAattempts to deduce your SLURM account. This may fail, in which case
-A, –accountneeds to be supplied.
-N,–nodesallows to reserve more than 1 node (the default). This may speed up the screening; see the limitations above.
-d,–dependency, list of comma separated jobids, the job will wait for to finish
-l,–runlimit, this defaults to 300 minutes.
-p,–partition, the default is
parallelon Mogon2, no smp-partition should be choosen.
-t,–threads, BWA can work in parallel. Please consult the manual. The default is 8.
-o,–outdiroutput directory path (default is the current working directory)
Barracuda is a GPU-accelerated implementation of BWA
Bowtie2 is a well known read aligner with a focus on gapped alignments.
As preliminary scaling tests indicate that the program can scale to a full node and is still reasonably fast, no wrapper script has been installed as a module, so far2). Instead, a few samples are given:
segemehl seems to be a pretty good alignment tool, mentioned here, due to the blog which is cited below.
There will be no wrapper script for
segemehl: If this comparison bears any truth, the software might be really good. But also pretty memory hungry. And several tens GB / core is just too mutch. If you want to try segemehl, be sure to write your own wrapper script (perhaps stage-in the reference to a local scratch, not the ramdisk) and reserve sufficient memory. Be aware that you will be accounted for the pro-longed run time and memory.
This part needs some more time to be finished ….