SPAdes 3.15.4
It’s all about the viruses: new coronaSPAdes, rnaviralSPAdes and metaviralSPAdes pipelines.
See changes in changelog
Download SPAdes binaries for Linux (64-bit only)
Download SPAdes binaries for MacOS
Manuals and support
- SPAdes manual with installation guide (ver 3.15.4)
- Same SPAdes manual in markdown
- rnaSPAdes manual
- truSPAdes manual (deprecated)
- SPAdes on GAGE-B data sets benchmark
- Benchmark for other data sets
If you have a problem running SPAdes you can look for a similar issue on our GitHub repository, create a new one or write us via e-mail: .
Note, that SPAdes binaries may not work on new Linux kernels.
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For the benchmarks we used:
- MDA single-cell E. coli; 6.3 Gb, 29M reads, 2x100bp, insert size ~ 270bp (Illumina Genome Analyzer IIx)
- Standard isolate E. coli; 6.2Gb, 28M reads, 2x100bp, insert size ~ 215bp (Illumina Genome Analyzer IIx), also available at NCBI SRA (ERR008613)
- MDA single-cell S. aureus; 14.6Gb, 33M reads, 2x100bp, insert size ~ 214bp (Illumina Genome Analyzer IIx)
More datasets as well as reference genomes are available here.
E. coli K-12 MG1655 reference length is 4639675 bp with 4324 annotated genes. S. aureus USA300 FPR3757 (chromosome and three plasmids) reference length is 2917469 bp with 2622 annotated genes.
Only contigs of 500 bp and longer were taken in consideration. Tables were obtained using QUAST 4.6.3.
Assembly | NG50 | # contigs | Largest | Total length | MA | MM | IND | GF (%) | # genes |
Single-cell E. coli | |||||||||
A5 | 14399 | 745 | 101584 | 4441145 | 3 | 11.92 | 0.19 | 89.867 | 3443 |
ABySS | 68534 | 179 | 178720 | 4345617 | 6 | 3.49 | 0.83 | 88.265 | 3704 |
CLC | 32506 | 503 | 113285 | 4656964 | 1 | 5.54 | 1.00 | 92.286 | 3767 |
EULER-SR | 26662 | 429 | 140518 | 4248713 | 12 | 9.98 | 20.17 | 84.846 | 3410 |
Ray | 45448 | 361 | 210820 | 4379139 | 16 | 5.29 | 1.24 | 88.345 | 3634 |
SOAPdenovo | 1540 | 1166 | 51517 | 2958144 | 1 | 1.49 | 0.11 | 57.668 | 1766 |
Velvet | 22648 | 261 | 132865 | 3501984 | 2 | 2.19 | 1.17 | 73.761 | 3079 |
E+V-SC | 32051 | 344 | 132865 | 4540286 | 2 | 2.26 | 0.70 | 91.727 | 3767 |
IDBA-UD contigs | 98306 | 244 | 284464 | 4814043 | 3 | 4.37 | 0.23 | 95.158 | 4041 |
IDBA-UD scaffolds | 109057 | 229 | 284464 | 4813609 | 3 | 4.42 | 0.75 | 95.145 | 4046 |
SPAdes 3.12 contigs | 105885 | 231 | 268283 | 4795250 | 3 | 2.02 | 0.30 | 94.853 | 4028 |
SPAdes 3.12 scaffolds | 117600 | 214 | 285212 | 4800301 | 3 | 2.41 | 0.61 | 94.886 | 4030 |
Isolate E. coli | |||||||||
A5 | 43651 | 176 | 181690 | 4551797 | 0 | 0.40 | 0.09 | 98.017 | 4163 |
ABySS | 106155 | 96 | 221861 | 4619631 | 2 | 3.72 | 0.37 | 98.969 | 4241 |
CLC | 86964 | 112 | 221549 | 4550314 | 1 | 0.99 | 0.18 | 98.057 | 4202 |
EULER-SR | 110153 | 100 | 221409 | 4574240 | 4 | 3.14 | 5.43 | 98.092 | 4182 |
Ray | 86246 | 98 | 221942 | 4634429 | 1 | 1.42 | 0.09 | 96.865 | 4136 |
SOAPdenovo | 49626 | 181 | 165487 | 4535469 | 0 | 0.15 | 0.09 | 97.696 | 4132 |
Velvet | 82776 | 120 | 242032 | 4554702 | 3 | 2.44 | 0.35 | 98.131 | 4190 |
E+V-SC | 54856 | 171 | 166115 | 4539639 | 0 | 1.30 | 0.11 | 97.792 | 4134 |
IDBA-UD contigs | 106844 | 110 | 221687 | 4565529 | 3 | 3.40 | 0.24 | 98.269 | 4200 |
IDBA-UD scaffolds | 133098 | 93 | 284363 | 4565454 | 4 | 4.08 | 0.55 | 98.282 | 4208 |
SPAdes 3.12 contigs | 125485 | 88 | 224545 | 4555008 | 1 | 1.93 | 0.18 | 98.092 | 4197 |
SPAdes 3.12 scaffolds | 133189 | 83 | 264976 | 4555437 | 1 | 1.98 | 0.22 | 98.090 | 4197 |
Single-cell S. aureus | |||||||||
A5 | 4829 | 937 | 41828 | 2770402 | 2 | 24.59 | 0.30 | 91.579 | 1815 |
ABySS | 43173 | 185 | 175286 | 2899223 | 3 | 6.46 | 0.50 | 96.572 | 2458 |
EULER-SR | 7247 | 750 | 66549 | 2988161 | 29 | 21.79 | 10.78 | 94.395 | 2009 |
Ray | 62026 | 84 | 125177 | 2947717 | 12 | 1.40 | 0.44 | 92.960 | 2410 |
SOAPdenovo | 510 | 1047 | 27317 | 1473402 | 0 | 1.32 | 0.29 | 46.717 | 595 |
Velvet | 15656 | 347 | 67677 | 2746768 | 3 | 4.41 | 4.27 | 93.181 | 2274 |
E+V-SC | 32296 | 215 | 107657 | 2932416 | 5 | 6.89 | 5.03 | 97.497 | 2476 |
IDBA-UD contigs | 87549 | 114 | 175236 | 2996997 | 4 | 2.47 | 0.76 | 98.658 | 2568 |
IDBA-UD scaffolds | 111392 | 99 | 210360 | 2996115 | 4 | 2.54 | 1.46 | 98.681 | 2574 |
SPAdes 3.12 contigs | 174343 | 79 | 329332 | 2992317 | 4 | 2.68 | 0.49 | 98.483 | 2582 |
SPAdes 3.12 scaffolds | 195326 | 75 | 429070 | 2993815 | 4 | 2.96 | 0.49 | 98.484 | 2582 |
A5 and CLC 3.22.55708 were run with default parameters. ABySS 1.3.5, EULER-SR 2.0.1, Ray 2.2.0, SOAPdenovo 2.04, Velvet 1.2.07, and E+V-SC were run with vertex size 55. IDBA-UD 1.1.0 was run in its default iterative mode.
Assembly | NG50 | # contigs | Largest | Total length | MA | MM | IND | GF (%) | # genes |
E. coli K-12 Illumina only | |||||||||
SPAdes 3.12 contigs | 125485 | 99 | 224454 | 4557432 | 0 | 2.53 | 0.33 | 98.136 | 4196 |
E. coli K-12 Illumina + PacBio P4 | |||||||||
SPAdes 3.12 contigs | 4640965 | 5 | 4640965 | 4643912 | 0 (6*) | 11.41 | 1.12 | 99.968 | 4320 |
SPAdes 3.12 scaffolds | 4640965 | 5 | 4640965 | 4643912 | 0 (6*) | 11.41 | 1.12 | 99.968 | 4320 |
- E. coli K-12 MG1655 Illumina standard isolate dataset outlined above
- E. coli K-12 MG1655 PacBio RS II C2/P4 dataset available from PacBio DevNet
Assembly | NG50 | # contigs | Largest | Total length | MA | MM | IND | GF (%) | # genes |
SPAdes 3.12 contigs | 133154 | 85 | 285138 | 4572473 | 3 | 3.44 | 3.39 | 98.459 | 4204 |
SPAdes 3.12 scaffolds | 133154 | 83 | 285138 | 4572673 | 3 | 3.44 | 3.39 | 98.459 | 4204 |
Acknowledgements
This work was supported by the Russian Science Foundation (grant 14-50-00069). Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the organizations or agencies that provided support for the project.