These are not the k-mers you are looking for: efficient online k-mer counting using a probabilistic data structure

K-mer abundance analysis is widely used for many purposes in nucleotide sequence analysis, including data preprocessing for de novo assembly, repeat detection, and sequencing coverage estimation. We present the khmer software package for fast and memory efficient online counting of k-mers in sequencing data sets. Unlike previous methods based on data structures such as hash tables, suffix arrays, and trie structures, khmer relies entirely on a simple probabilistic data structure, a Count-Min Sketch. The Count-Min Sketch permits online updating and retrieval of k-mer counts in memory which is necessary to support online k-mer analysis algorithms. On sparse data sets this data structure is considerably more memory efficient than any exact data structure. In exchange, the use of a Count-Min Sketch introduces a systematic overcount for k-mers; moreover, only the counts, and not the k-mers, are stored. Here we analyze the speed, the memory usage, and the miscount rate of khmer for generating k-mer frequency distributions and retrieving k-mer counts for individual k-mers. We also compare the performance of khmer to several other k-mer counting packages, including Tallymer, Jellyfish, BFCounter, DSK, KMC, Turtle and KAnalyze. Finally, we examine the effectiveness of profiling sequencing error, k-mer abundance trimming, and digital normalization of reads in the context of high khmer false positive rates. khmer is implemented in C++ wrapped in a Python interface, offers a tested and robust API, and is freely available under the BSD license at github.com/ged-lab/khmer

Fast and Powerful Hashing using Tabulation

Randomized algorithms are often enjoyed for their simplicity, but the hash functions employed to yield the desired probabilistic guarantees are often too complicated to be practical. Here we survey recent results on how simple hashing schemes based on tabulation provide unexpectedly strong guarantees. Simple tabulation hashing dates back to Zobrist [1970]. Keys are viewed as consisting of $c$ characters and we have precomputed character tables $h_1,...,h_c$ mapping characters to random hash values. A key $x=(x_1,...,x_c)$ is hashed to $h_1[x_1] \oplus h_2[x_2].....\oplus h_c[x_c]$. This schemes is very fast with character tables in cache. While simple tabulation is not even 4-independent, it does provide many of the guarantees that are normally obtained via higher independence, e.g., linear probing and Cuckoo hashing. Next we consider twisted tabulation where one input character is "twisted" in a simple way. The resulting hash function has powerful distributional properties: Chernoff-Hoeffding type tail bounds and a very small bias for min-wise hashing. This also yields an extremely fast pseudo-random number generator that is provably good for many classic randomized algorithms and data-structures. Finally, we consider double tabulation where we compose two simple tabulation functions, applying one to the output of the other, and show that this yields very high independence in the classic framework of Carter and Wegman [1977]. In fact, w.h.p., for a given set of size proportional to that of the space consumed, double tabulation gives fully-random hashing. We also mention some more elaborate tabulation schemes getting near-optimal independence for given time and space. While these tabulation schemes are all easy to implement and use, their analysis is not

Closing the Gap Between Short and Long XORs for Model Counting

Many recent algorithms for approximate model counting are based on a reduction to combinatorial searches over random subsets of the space defined by parity or XOR constraints. Long parity constraints (involving many variables) provide strong theoretical guarantees but are computationally difficult. Short parity constraints are easier to solve but have weaker statistical properties. It is currently not known how long these parity constraints need to be. We close the gap by providing matching necessary and sufficient conditions on the required asymptotic length of the parity constraints. Further, we provide a new family of lower bounds and the first non-trivial upper bounds on the model count that are valid for arbitrarily short XORs. We empirically demonstrate the effectiveness of these bounds on model counting benchmarks and in a Satisfiability Modulo Theory (SMT) application motivated by the analysis of contingency tables in statistics.Comment: The 30th Association for the Advancement of Artificial Intelligence (AAAI-16) Conferenc

More Analysis of Double Hashing for Balanced Allocations

With double hashing, for a key $x$, one generates two hash values $f(x)$ and $g(x)$, and then uses combinations $(f(x) +i g(x)) \bmod n$ for $i=0,1,2,...$ to generate multiple hash values in the range $[0,n-1]$ from the initial two. For balanced allocations, keys are hashed into a hash table where each bucket can hold multiple keys, and each key is placed in the least loaded of $d$ choices. It has been shown previously that asymptotically the performance of double hashing and fully random hashing is the same in the balanced allocation paradigm using fluid limit methods. Here we extend a coupling argument used by Lueker and Molodowitch to show that double hashing and ideal uniform hashing are asymptotically equivalent in the setting of open address hash tables to the balanced allocation setting, providing further insight into this phenomenon. We also discuss the potential for and bottlenecks limiting the use this approach for other multiple choice hashing schemes.Comment: 13 pages ; current draft ; will be submitted to conference shortl

A unified approach to linear probing hashing with buckets

We give a unified analysis of linear probing hashing with a general bucket size. We use both a combinatorial approach, giving exact formulas for generating functions, and a probabilistic approach, giving simple derivations of asymptotic results. Both approaches complement nicely, and give a good insight in the relation between linear probing and random walks. A key methodological contribution, at the core of Analytic Combinatorics, is the use of the symbolic method (based on q-calculus) to directly derive the generating functions to analyze.Comment: 49 page