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Background For single-cell or metagenomic sequencing projects, it is necessary to sequence with a very high mean coverage in order to make sure that all parts of the sample DNA get covered by the reads produced. This leads to huge datasets with lots of redundant data. A filtering of this data prior to assembly is advisable. Brown et al. (2012) presented the algorithm Diginorm for this purpose, which filters reads based on the abundance of their k-mers. Methods We present Bignorm, a faster and quality-conscious read filtering algorithm. An important new algorithmic feature is the use of phred quality scores together with a detailed analysis of the k-mer counts to decide which reads to keep. Results We qualify and recommend parameters for our new read filtering algorithm. Guided by these parameters, we remove in terms of median 97.15% of the reads while keeping the mean phred score of the filtered dataset high. Using the SDAdes assembler, we produce assemblies of high quality from these filtered datasets in a fraction of the time needed for an assembly from the datasets filtered with Diginorm. Conclusions We conclude that read filtering is a practical and efficient method for reducing read data and for speeding up the assembly process. This applies not only for single cell assembly, as shown in this paper, but also to other projects with high mean coverage datasets like metagenomic sequencing projects. Our Bignorm algorithm allows assemblies of competitive quality in comparison to Diginorm, while being much faster. Bignorm is available for download at https://git.informatik.uni-kiel.de/axw/Bignorm. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1724-7) contains supplementary material, which is available to authorized users.

Als erstes Schwerpunktprogramm bekommt das DFG SPP 1307 ,,Algorithm Engineering“ durch deutsch-indische Projekte eine binationale Komponente. Die Zusammenarbeit in der 3. Phase des Schwerpunktprogrammes umfasst Optimierung im Schienenverkehr, Berechnungen unter Unsicherheiten, Algorithmen fur Datenstrome und parallele quantum-evolutionare Algorithmen.

We present the first deterministic 1+e approximation algorithm for finding a large matching in a bipartite graph in the semi-streaming model which requires only O((1/e)5) passes over the input stream. In this model, the input graph G=(V,E) is given as a stream of its edges in some arbitrary order, and storage of the algorithm is bounded by O(npolylog n) bits, where $n = \lvert {V}\rvert $. The only previously known arbitrarily good approximation for general graphs is achieved by the randomized algorithm of McGregor (Proceedings of the International Workshop on Approximation Algorithms for Combinatorial Optimization Problems and Randomization and Computation, Berkeley, CA, USA, pp. 170–181, 2005), which uses Ω((1/e)1/e ) passes. We show that even for bipartite graphs, McGregor’s algorithm needs Ω(1/e) Ω(1/e) passes, thus it is necessarily exponential in the approximation parameter. The design as well as the analysis of our algorithm require the introduction of some new techniques. A novelty of our algorithm is a new deterministic assignment of matching edges to augmenting paths which is responsible for the complexity reduction, and gets rid of randomization. We repeatedly grow an initial matching using augmenting paths up to a length of 2k+1 for k=⌈2/e⌉. We terminate when the number of augmenting paths found in one iteration falls below a certain threshold also depending on k, that guarantees a 1+e approximation. The main challenge is to find those augmenting paths without requiring an excessive number of passes. In each iteration, using multiple passes, we grow a set of alternating paths in parallel, considering each edge as a possible extension as it comes along in the stream. Backtracking is used on paths that fail to grow any further. Crucial are the so-called position limits: when a matching edge is the ith matching edge in a path and it is then removed by backtracking, it will only be inserted into a path again at a position strictly lesser than i. This rule strikes a balance between terminating quickly on the one hand and giving the procedure enough freedom on the other hand.