Many short read aligners have been developed in the last two years, but few are widely used nowadays. For most people who are not familiar with algorithms, the adoption of an aligner is largely determined by its popularity. Heavily used aligners almost certainly have fewer bugs and deliver better practical performance. If you have questions, you are more likely to get answers from others. How can an aligner gain its popularity? There are many reasons, but to me, the key is its practibility which is a combination of several factors including speed, features and memory. Although practical aligners may not be always popular due to timing, licensing or other subtle and complicated issues, popular aligners are always practical. No exceptions.

This article largely reflects the philosophy behind my own aligners, maq and bwa. It focuses on short-read aligners but many claims are also applicable to other high-performance tools in bioinformatics.

Popular Short-read Aligners

Before going into details on how practibility is achieved, I give a list of aligners that are widely used to the best of my knowledge. The list may be biased due to my own limitations, but it is a reasonable start, anyway.

Probably the most frequently cited short read aligner is MAQ, my first short read aligner. It has been used in several high-profile papers and large-scale projects. However, the development of maq is very slow in the last year as my focus is shifted to BWA which has several advantages over maq. Nonetheless, maq may still occassionally outperform bwa in a few aspects and that is why maq is not retired yet.

SOAP is the first published short read aligner. It used to be widely used given its capability of finding short indels on single-end reads, but not at present due to the development of other new aligners as well as its successor SOAP2.

Bowtie is popular due to its efficiency, flexibility and active maintainance, although I am always a little concerned about its default behaviour (I believe "--best -k 2" is better).

NovoAlign is a commercial software, but you are allowed to use its binary freely as long as you aim to publish your results. Novoalign is the most accurate in my benchmark done half a year ago. It is actively maintained and highly feature rich. A potential concern to me is its free version does not support multithreading which may cause some difficulties in running it in large scale.

Aligners such as Bfast, Mosaik, mrFast and SeqMap are also mentioned in some publications and/or forums, but my impression is they have not reached the popularity of maq, bowtie, bwa and soap/soap2 due to timing and various other reasons.

Being Practical


For an aligner, speed is always the first thing that comes to our sight and the first thing developers care about. It is largely determined by the algorithm. People all have paid enough attention to this factor, although sometimes too much.

Feature set

To me, the completeness of feature sets outweighs the speed in evaluating an aligner. A practical short-read aligner must be able to work with >100bp reads, perform paired-end mapping, tolerate moderately high error rate and support the standard formats (e.g. FASTQ and SAM). Doing gapped alignment becomes more and more important with the increasing read lengths. Other features like capability of non-standard alignment (e.g. bisulfite alignment), adapter trimming, low-quality trimming and more are not mandatory but also likely to increase the popularity.

Unfortunately, not many developers have paid enough attention to the feature set of their aligners and some even trade features for speed (e.g. only allowing very short reads), which makes a lot of aligners less useful in practice, even when they are published.


The importance of the memory usage of an aligner is frequently overlooked at the beginning but quickly rediscovered when the aligner is put into use in large scale.

Nowadays, 8-core computers with 16GB memory are pretty affordable and widely used. In most large sequencing centers (at least the ones I have been to), 32GB and 64GB machines are rare due to their relatively high cost. This means a reasonable aligner should not use more than ~12GB memory to leave some memory for other jobs running on the 16GB machine. And for aligners using more than 4GB memory, multithreading becomes necessary; otherwise we could hardly use the computing resources effectively given the memory limit. Nonetheless, even with multithreading, memory below 7GB in total is still preferred when the aligner is used in a large compute farm because the average load of a farm is descreased given many multithreading jobs which increase the idle time in waiting enough CPU slots.

Running jobs on a large compute farm involes more practical concerns than on a single computer, and attracting users on such farms is really the short-cut to popularize an aligner. Even for users working on a single computer, small memory usage is frequently much more friendly and affordable.

To be practical, an aligner should even trade speed for memory, although some developers do the reverse to show good results in their speed benchmark. But ultimately, memory hungry aligners will be faced with problems even if they get published.