Software for de novo genome assembly and other bioinformatics tasks.
Benchmark result for human transcriptomics. See more.
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.
Find variants that will not be detected by other methods (de-novo or mapping), like large indels. Find also genome rearrangements more easily.
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.
Discover how s-aligner can help you in different situations.
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| LGA50 | NGA50 | Genome fraction (%) | Max contig length | Largest alignment | Misassembled length | |
|---|---|---|---|---|---|---|
| Velvet | it doesn't contain contigs >= 500 bp | |||||
| SPAdes | - | - | 0,72 | 880 | 77 | 0 |
| rnaSPAdes | 3 | 1.642 | 98,04 | 4.070 | 2.848 | 33.248 |
| s-aligner | 1 | 10.155 | 99,90 | 10.263 | 10.155 | 24.483 |
Assembly of run SRR12956185 PCR-free deep-sequencing of ZIKV-DAK-41524 (10.657 bp)
| LGA50 | NGA50 | Genome fraction (%) | Max contig length | Largest alignment | Misassembled length | |
|---|---|---|---|---|---|---|
| Velvet | Assembles another present phage with contigs under 2.500 bp and only covering 82% of the reference | |||||
| SPAdes | 4 | 5.529 | 95,14 | 68.745 | 19.436 | 0 |
| rnaSPAdes | 1 | 58.498 | 100 | 58.723 | 58.498 | 0 |
| s-aligner | 1 | 68.986 | 100 | 69.327 | 68.986 | 0 |
Assembly of run SRR12644168 Sequencing of Mycobacterium phage Mecca: Illumina Reads (68.890 bp)
| LGA50 | NGA50 | Genome fraction (%) | Max contig length | Largest alignment | Misassembled length | |
|---|---|---|---|---|---|---|
| rnaSPAdes | 3 | 4.980 | 98,47 | 7.385 | 7.357 | 11.877 | s-aligner | 1 | 29.299 | 98,94 | 29.400 | 29.299 | 0 |
Assembly of run SRR12445029 Ion torrent sequencing of SARS-Cov-2 virus
With s-aligner you can:
Variants found in a simulated SARS-Cov-2 sample mapping raw reads to the reference for variant calling.
Variants found in a simulated SARS-Cov-2 sample maoping contigs obtained by s-aligner to the reference for variant calling. The large indel was really present in the sample.
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 | 26609 | 17066 | 73587 | 43675 | 117262 |
| Transcripts > 500 bp | 8893 | 8801 | 13469 | 17694 | 31163 |
| Transcripts > 1000 bp | 2904 | 2310 | 2615 | 5214 | 7829 |
| Avg. mismatches per transcript | 6.023 | 8.441 | 4.93 | 7.05 | 5.698 |
| Database coverage | 0.019 | 0.025 | 0.025 | 0.025 | 0.034 |
| 50%-assembled genes | 3041 | 2948 | 3363 | 3661 | 4237 |
| 95%-assembled genes | 573 | 461 | 450 | 740 | 839 |
Improved performance for viral and bacterial genome assembly
A mapping tool that does not break the reads in pieces. Useful for inspection of reads in a run.
Assemble transcriptome runs the same way than genome runs. Assemble only selected transcripts for faster results.
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.
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.
For unlimited licenses or packs of floating licenses please contact us. See the terms for more information.