SPAdes 2.4

SPAdes Assembler SPAdes manual with installation guide (ver 2.4.0)

Support e-mail: spades.support@bioinf.spbau.ru

SPAdes 2.4 is out!

See all changes in changelog.

For the benchmark 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)

E. coli K-12 MG1655 reference length is 4639675 with 4324 annotated genes. Only contigs of 500bp and longer were taken in consideration.

Assembly	NG50	# contigs	Largest contig	Total length	# misassemblies	# mismatches per 100 kbp	# indels per 100 kbp	Genome fraction (%)	# genes
Single-cell E. coli
A5	14399	745	101584	4441145	8	11.68	0.17	89.681	3439
ABySS	68534	179	178720	4345617	6	3.32	1.69	88.254	3703
CLC	32506	503	113285	4656964	2	5.54	1.43	92.211	3766
EULER-SR	26662	429	140518	4248713	17	10.85	35.69	84.856	3416
Ray	55395	296	210612	4649552	14	6.08	0.61	91.771	3826
SOAPdenovo	18468	569	87533	4098032	7	116.37	7.48	79.807	3037
Velvet	22648	261	132865	3501984	2	1.93	1.23	73.574	3072
E+V-SC	32051	344	132865	4540286	2	2.14	0.73	91.488	3759
IDBA1.1_contig	98306	244	284464	4814043	8	5.06	0.27	94.896	4035
IDBA1.1_scaffold	109057	229	284464	4813610	8	4.97	0.89	94.923	4040
SPAdes2.4_contigs	110539	277	269177	4877521	2	5.27	0.79	95.622	4047
SPAdes2.4_scaffolds	112120	250	269177	4910892	4	6.58	1.33	95.698	4055

Isolate E. coli
A5	43651	176	181690	4551797	0	0.26	0.11	97.787	4154
ABySS	106155	96	221861	4619631	2	3.66	0.41	98.871	4239
CLC	86964	112	221549	4550314	1	1.79	0.31	97.799	4186
EULER-SR	110153	100	221409	4574240	8	2.49	10.15	97.846	4180
Ray	83128	113	221942	4563341	2	2.18	0.18	97.937	4185
SOAPdenovo	62512	141	172567	4519621	0	27.26	4.69	97.345	4134
Velvet	82776	120	242032	4554702	3	2.36	0.37	97.864	4185
E+V-SC	54856	171	166115	4539639	0	1.26	0.13	97.465	4124
IDBA1.1_contig	106844	110	221687	4565529	3	2.99	0.31	97.992	4195
IDBA1.1_scaffold	133098	93	284363	4565454	4	3.61	0.59	98.021	4204
SPAdes2.4_contigs	134076	97	285228	4634583	2	2.99	0.57	98.916	4245
SPAdes2.4_scaffolds	134076	97	285228	4635776	2	3.92	0.59	98.937	4245

ABySS 1.3.4, EULER-SR 2.0.1, Ray 2.0.0, Velvet, and E+V-SC were run with vertex size 55. A5 and CLC 3.22.55708 were run with default parameters. SOAPdenovo 1.0.4 was run with vertex size 27–31. IDBA 1.1.0 was run in its default iterative mode. The total assembly size may increase (and in some cases exceeds the genome size) due to contaminants (see Chitsaz et al. (2011)), misassembled contigs, repeats, and hubs that contribute to multiple contigs. The percentage of the E. coli genome covered filters out these issues (Genome fraction (%) column). The NG50 statistic is the same as the N50 except that the genome size is used rather than the assembly size. Misassemblies are locations on an assembled contig where the left flanking sequence aligns over 1 kb away from the right flanking sequence on the reference. Mismatch (substitution) error rate and number of indels are measured in aligned regions of the contigs. In each column, the best assembler by that criteria is indicated in bold.

Related publications

Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey A. Gurevich, Mikhail Dvorkin, Alexander S. Kulikov, Valery M. Lesin, Sergey I. Nikolenko, Son Pham, Andrey D. Prjibelski, Alexey V. Pyshkin, Alexander V. Sirotkin, Nikolay Vyahhi, Glenn Tesler, Max A. Alekseyev, and Pavel A. Pevzner. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. Journal of Computational Biology 19(5) (2012), 455-477. doi:10.1089/cmb.2012.0021
Son K. Pham, Dmitry Antipov, Alexander Sirotkin, Glenn Tesler, Pavel A. Pevzner, and Max A. Alekseyev. Pathset Graphs: A Novel Approach for Comprehensive Utilization of Paired Reads in Genome Assembly. Journal of Computational Biology (2012). doi:10.1089/cmb.2012.0098

Nikolay Vyahhi, Son K. Pham, and Pavel A. Pevzner. From de Bruijn Graphs to Rectangle Graphs for Genome Assembly. Lecture Notes in Bioinformatics 7534 (2012), pp. 249-261. doi:10.1007/978-3-642-33122-0_20
Sergey I. Nikolenko, Anton I. Korobeynikov and Max. A. Alekseyev. BayesHammer: Bayesian clustering for error correction in single-cell sequencing. BMC Genomics (2013) 14(S1):S7. doi:10.1186/1471-2164-14-S1-S7

Acknowledgements

This work was supported by the Government of the Russian Federation (grant 11.G34.31.0018) and by the National Institutes of Health, USA (NIH grant 3P41RR024851-02S1). 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.

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