Contignant s-aligner

Software for de novo genome assembly and other bioinformatics tasks.

Benchmark result for human transcriptomics. See more.

Larger assemblies

Assemblies obtained from s-aligner are always on par or better than assemblies obtained with any other available software (SPAdes, Velvet, etc...). On average we get 110% larger NG50 for viral genomes and 64% larger for other ones. And even if you use single reads you outperform assemblies generated with paired-end reads. This way you can cut in half your costs without losing quality.

Improved variant-calling

Find variants that will not be detected by other methods (de-novo or mapping), like large indels. Find also genome rearrangements more easily.

Transparent results

Get quality scores for every base pair in your assemblies and visually inspect how every read was used to obtain the assemblies. No black-box results but understandable results. Develop flexible incremental strategies to achieve results adapted to your needs.

Introducing s-aligner

Some use cases

Discover how s-aligner can help you in different situations.

Assembly of genomes: comparing performance

s-aligner usually obtains the best results of any de-novo assembly software.

There are cases in which s-aligner notoriously outperforms any other de-novo genome-assembly software. See some of these cases on the slider.

See benchmarks

Discerning variants and rearrangements

With s-aligner you can:

  • Get large indels that are usually missed by mon-de-novo methods.
  • See exactly how the contigs obtained by s-aligner were ensembled.
  • Align the contigs to a reference (for example, using Quast) and compare rearrangement possibilities.

Assembly of transcriptomes: comparing performance

s-aligner performance for a human transcriptome sample.

36% increase in database coberture: you get more transcripts, covering a bigger proportion of the human transcriptome, and with larger transcripts.

See benchmarks
rnaSPAdes Megahit s-aligner rnaSPAdes + Mehahit s-aligner + rnaSPAdes + Megahit
Transcripts > 500 bp88938801134691769431163
Transcripts > 1000 bp29042310261552147829
Avg. mismatches per transcript6.0238.4414.937.055.698
Database coverage0.0190.0250.0250.0250.034
50%-assembled genes30412948336336614237
95%-assembled genes573461450740839
De novo assembly

Improved performance for viral and bacterial genome assembly

Reference mapping

A mapping tool that does not break the reads in pieces. Useful for inspection of reads in a run.

Transcriptome de novo assembly

Assemble transcriptome runs the same way than genome runs. Assemble only selected transcripts for faster results.

Multiple functionality included

Not only genome assembly. Can be used for reference mapping, or for transcriptome de novo assembly. More functionalities to be added in next software updates.

Easily integrate into any pipeline

Works as command line application (Linux and DOS). Easily integrate into any pipeline. Uses popular data formats like FASTA or FASTQ.


Contact us by email or join our community to get answers to your doubts. We'd like to learn from you how to improve our software.


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For unlimited licenses or packs of floating licenses please contact us. See the terms for more information.




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