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  2. SAMtools - Wikipedia

    en.wikipedia.org/wiki/SAMtools

    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

  3. SAM (file format) - Wikipedia

    en.wikipedia.org/wiki/SAM_(file_format)

    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.

  4. Binary Alignment Map - Wikipedia

    en.wikipedia.org/wiki/Binary_Alignment_Map

    Binary Alignment Map (BAM) is the comprehensive raw data of genome sequencing; [1] it consists of the lossless, compressed binary representation of the Sequence Alignment Map-files. [2] [3] BAM is the compressed binary representation of SAM (Sequence Alignment Map), a compact and index-able representation of nucleotide sequence alignments. [4]

  5. Pileup format - Wikipedia

    en.wikipedia.org/wiki/Pileup_format

    www.htslib.org /doc /samtools-mpileup.html 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.

  6. Sorting algorithm - Wikipedia

    en.wikipedia.org/wiki/Sorting_algorithm

    Insertion sort is widely used for small data sets, while for large data sets an asymptotically efficient sort is used, primarily heapsort, merge sort, or quicksort. Efficient implementations generally use a hybrid algorithm , combining an asymptotically efficient algorithm for the overall sort with insertion sort for small lists at the bottom ...

  7. Variant Call Format - Wikipedia

    en.wikipedia.org/wiki/Variant_Call_Format

    The 1-based position of the variation on the given sequence. 3: ID: The identifier of the variation, e.g. a dbSNP rs identifier, or if unknown a ".". Multiple identifiers should be separated by semi-colons without white-space. 4: REF: The reference base (or bases in the case of an indel) at the given position on the given reference sequence. 5: ALT

  8. Z-order curve - Wikipedia

    en.wikipedia.org/wiki/Z-order_curve

    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.

  9. Integer sorting - Wikipedia

    en.wikipedia.org/wiki/Integer_sorting

    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]