Choosing mapper


Bowtie2 is a widely used mapping tool that is well suited for mapping reads to reasonably large databases and is commonly used for mapping to the human genome. As Bowtie2 requires a pre-constructed index its use in Tentacle is best suited when comparing to a single large database of reference sequences. It is implemented in Tentacle mainly as a reliable tool to perform filtering of human reads from metagenomic samples. Our testing showed that Bowtie2 was unable to handle a case with a very large reference database (7.5 GiB in FASTA format). Bowtie2 is parallelized to take advantage of several CPUs.


GEM has implemented a mapping algorithm that also requires the construction of a pre-computed index. GEM was the only software in our testing that was capable of handling our largest test database weighing in at 7.5 GiB containing 11.5 million sequences in FASTA format. The GEM paper explains that GEM provides “fully tunable exhaustive searches that return all existing matches, including gapped ones”. GEM is parallelized and can take advantage of several CPUs.


pBLAT is a parallelized version of the widely used BLAT tool. The parallelization allows pBLAT to utilize several CPUs on a single computer in a way that the original BLAT tool is unable to. The pBLAT website states “It can reduce run time linearly, and use almost equal memory as the original blat program”. As pBLAT does not require a precomputed index it is well suited for e.g. mapping metagenomic samples to their assembled contings, which otherwise would require preparing many separate indexes if mapping with other mappers.

RazerS 3

RazerS 3 is a mapper that implements an algorithm that is well suited for aligning long reads with high error rates. RazerS 3 does not require a precomputed index, thus making it applicable in cases where metagenomic samples are mapped to their assembled contigs, just like e.g. pBLAT. The RazerS 3 publication shows that RazerS 3 often displays superior sensitivity when compared to other mappers. RazerS 3 is parallelised and can utilize several CPUs.


USEARCH is a widely used sequence alignment software that implements many BLAST-like sequence alignment options with a significantly higher speed and comparable sensitivity. The algorithm can create database indexes on-the-fly but can also precompute indexes to save time in cases where the same reference is used for all samples. USEARCH can utilize several CPUs and is capable of performing translated searches (e.g. searching with nucleotide reads against a protein database), making it very useful for quantifying the presence of specific genes in a metagenomic dataset.


NCBI BLAST is a ubiquitous alignment algorithm that requires little introduction and capable of many different types of queries. It is not parallelized (however, as previously mentioned, some parallelized implementations such as mpiBLAST do exist). A mapping module for BLAST is included in Tentacle because it is widely used and the existence of such a module enables researchers that already use BLAST in their workflows to try out Tentacle without modifying too much of the workflow. However, we strongly discourage the use of BLAST because of its relatively slow speed compared to the previously described algorithms that can be hundreds of times faster than BLAST. Tentacle allows users that require the use of BLAST to essentially reduce the computation time by a factor of N, where N is the number of nodes used (as seen in the scaling evaluation).