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sort samtools sort -o sorted_out unsorted_in.bam. Read the specified unsorted_in.bam as input, sort it by aligned read position, and write it out to sorted_out. Type of output can be either sam, bam, or cram, and will be determined automatically by sorted_out's file-extension. samtools sort -m 5000000 unsorted_in.bam sorted_out
Pileup format is a text-based format for summarizing the base calls of aligned reads to a reference sequence. This format facilitates visual display of SNP /indel calling and alignment. It was first used by Tony Cox and Zemin Ning at the Wellcome Trust Sanger Institute , and became widely known through its implementation within the SAMtools ...
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.
The binary equivalent of a SAM file is a Binary Alignment Map (BAM) file, which stores the same data in a compressed binary representation. [4] SAM files can be analysed and edited with the software SAMtools. [1] The header section must be prior to the alignment section if it is present.
In computer science, integer sorting is the algorithmic problem of sorting a collection of data values by integer keys. Algorithms designed for integer sorting may also often be applied to sorting problems in which the keys are floating point numbers, rational numbers, or text strings. [1]
Sorted arrays are the most space-efficient data structure with the best locality of reference for sequentially stored data. [citation needed]Elements within a sorted array are found using a binary search, in O(log n); thus sorted arrays are suited for cases when one needs to be able to look up elements quickly, e.g. as a set or multiset data structure.
The Z-ordering can be used to efficiently build a quadtree (2D) or octree (3D) for a set of points. [5] [6] The basic idea is to sort the input set according to Z-order.Once sorted, the points can either be stored in a binary search tree and used directly, which is called a linear quadtree, [7] or they can be used to build a pointer based quadtree.
Given a function that accepts an array, a range query (,) on an array = [,..,] takes two indices and and returns the result of when applied to the subarray [, …,].For example, for a function that returns the sum of all values in an array, the range query (,) returns the sum of all values in the range [,].