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  2. SAMtools - Wikipedia

    en.wikipedia.org/wiki/SAMtools

    samtools sort -m 5000000 unsorted_in.bam sorted_out Read the specified unsorted_in.bam as input, sort it in blocks up to 5 million k (5 Gb) [ units verification needed ] and write output to a series of bam files named sorted_out.0000.bam , sorted_out.0001.bam , etc., where all bam 0 reads come before any bam 1 read, etc. [ verification needed ]

  3. 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.

  4. Variant Call Format - Wikipedia

    en.wikipedia.org/wiki/Variant_Call_Format

    The Variant Call Format or VCF is a standard text file format used in bioinformatics for storing gene sequence or DNA sequence variations. The format was developed in 2010 for the 1000 Genomes Project and has since been used by other large-scale genotyping and DNA sequencing projects.

  5. 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.

  6. 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.

  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...

    S-MART handles mapped RNA-Seq data, and performs essentially data manipulation (selection/exclusion of reads, clustering and differential expression analysis) and visualization (read information, distribution, comparison with epigenomic ChIP-Seq data). It can be run on any laptop by a person without computer background.

  9. Selection algorithm - Wikipedia

    en.wikipedia.org/wiki/Selection_algorithm

    As a baseline algorithm, selection of the th smallest value in a collection of values can be performed by the following two steps: . Sort the collection; If the output of the sorting algorithm is an array, retrieve its th element; otherwise, scan the sorted sequence to find the th element.