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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. 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]

  4. 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.

  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. Help:Sortable tables - Wikipedia

    en.wikipedia.org/wiki/Help:Sortable_tables

    Datatype auto detection is inconsistent. That is why ISO date sorting works best with data-sort-type=isoDate added to the column header. It also avoids problems when only one digit is used for the month or day. Leading zeros are no longer needed. All tables below have data-sort-type=isoDate added to the column headers.

  7. Database index - Wikipedia

    en.wikipedia.org/wiki/Database_index

    In most cases, an index is used to quickly locate the data records from which the required data is read. In other words, the index is only used to locate data records in the table and not to return data. A covering index is a special case where the index itself contains the required data fields and can answer the required data. Consider the ...

  8. List of RNA-Seq bioinformatics tools - Wikipedia

    en.wikipedia.org/wiki/List_of_RNA-Seq...

    It uses the seed-and-vote mapping paradigm to determine the mapping location of the read by using its largest mappable region. It automatically decides whether the read should be globally mapped or locally mapped. For RNA-seq data, Subread should be used for the purpose of expression analysis. Subread can also be used to map DNA-seq reads.

  9. 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.