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fastqp Simple FASTQ quality assessment using Python. Kraken: [9] A set of tools for quality control and analysis of high-throughput sequence data. HTSeq [10] The Python script htseq-qa takes a file with sequencing reads (either raw or aligned reads) and produces a PDF file with useful plots to assess the technical quality of a run.
Intuitively, an extractor takes a weakly random n-bit input and a short, uniformly random seed and produces an m-bit output that looks uniformly random. The aim is to have a low d {\displaystyle d} (i.e. to use as little uniform randomness as possible) and as high an m {\displaystyle m} as possible (i.e. to get out as many close-to-random bits ...
Timsort sorts the list in time linearithmic (proportional to a quantity times its logarithm) in the list's length (()), but has a space requirement linear in the length of the list (()). If large lists must be sorted at high speed for a given application, timsort is a better choice; however, if minimizing the memory footprint of the sorting ...
SciPy (pronounced / ˈ s aɪ p aɪ / "sigh pie" [2]) is a free and open-source Python library used for scientific computing and technical computing. [3]SciPy contains modules for optimization, linear algebra, integration, interpolation, special functions, FFT, signal and image processing, ODE solvers and other tasks common in science and engineering.
Make a k-letter word list of the query sequence. Take k=3 for example, we list the words of length 3 in the query protein sequence (k is usually 11 for a DNA sequence) "sequentially", until the last letter of the query sequence is included. The method is illustrated in figure 1. Fig. 1 The method to establish the k-letter query word list. [14]
Multiple definitions of the term "batch effect" have been proposed in the literature. Lazar et al. (2013) noted, "Providing a complete and unambiguous definition of the so-called batch effect is a challenging task, especially because its origins and the way it manifests in the data are not completely known or not recorded."
Library multi-versioning (LMV): the entire programming library is duplicated for many instruction set extensions, and the operating system or the program decides which one to load at run-time. FMV, manually coded in assembly language, is quite commonly used in a number of performance-critical libraries such as glibc and libjpeg-turbo.
A Fenwick tree or binary indexed tree (BIT) is a data structure that stores an array of values and can efficiently compute prefix sums of the values and update the values. It also supports an efficient rank-search operation for finding the longest prefix whose sum is no more than a specified value.