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  2. List of sequence alignment software - Wikipedia

    en.wikipedia.org/wiki/List_of_sequence_alignment...

    Version 0.2 of October 2016, supports the algorithms BWA-MEM, BWA-backtrack, and BWA-ALN. All of them work with single-reads and paired-end reads. Yes Low quality bases trimming Yes Yes Free, GPL 3 [57] 2016 SSAHA, SSAHA2 Fast for a small number of variants Proprietary, freeware for academic and noncommercial use Stampy For Illumina reads.

  3. List of RNA-Seq bioinformatics tools - Wikipedia

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

    It is already adapted to align long reads (third-generation sequencing technologies) and can reach speeds of 45 million paired reads per hour per processor. [49] Subjunc [44] is a specialized version of Subread. It uses all mappable regions in an RNA-seq read to discover exons and exon-exon junctions.

  4. DNA sequencer - Wikipedia

    en.wikipedia.org/wiki/DNA_sequencer

    The GS FLX+ System promises read lengths of approximately 1000 base pairs while the GS Junior System promises 400 base pair reads. [ 12 ] [ 13 ] A predecessor to GS FLX+, the 454 GS FLX Titanium system was released in 2008, achieving an output of 0.7G of data per run, with 99.9% accuracy after quality filter, and a read length of up to 700bp.

  5. Read (biology) - Wikipedia

    en.wikipedia.org/wiki/Read_(biology)

    Sequencing technologies vary in the length of reads produced. Reads of length 20-40 base pairs (bp) are referred to as ultra-short. [2] Typical sequencers produce read lengths in the range of 100-500 bp. [3] However, Pacific Biosciences platforms produce read lengths of approximately 1500 bp. [4] Read length is a factor which can affect the results of biological studies. [5]

  6. Linked-read sequencing - Wikipedia

    en.wikipedia.org/wiki/Linked-read_sequencing

    Linked-read sequencing technology labels all reads that originate from the same long DNA fragment with the same barcode, so it enables the detection of a large number of structural variants. [4] Complexity of structural variants can be resolved with linked-read sequencing, and provide a complete picture of the genomic landscape.

  7. Coverage (genetics) - Wikipedia

    en.wikipedia.org/wiki/Coverage_(genetics)

    Sequence coverage (or depth) is the number of unique reads that include a given nucleotide in the reconstructed sequence. [1] [2] Deep sequencing refers to the general concept of aiming for high number of unique reads of each region of a sequence. [3] Physical coverage, the cumulative length of reads or read pairs expressed as a multiple of ...

  8. FASTQ format - Wikipedia

    en.wikipedia.org/wiki/FASTQ_format

    Reordering-based FASTQ compressors first cluster reads that share long substrings and then independently compress reads in each cluster after reordering them or assembling them into longer contigs, achieving perhaps the best trade-off between the running time and compression rate. SCALCE is the first such tool, followed by Orcom and Mince.

  9. Massive parallel sequencing - Wikipedia

    en.wikipedia.org/wiki/Massive_parallel_sequencing

    While single-read accuracy is 87%, consensus accuracy has been demonstrated at 99.999% with multi-kilobase read lengths. [ 37 ] [ 38 ] In 2015, Pacific Biosciences released a new sequencing instrument called the Sequel System, which increases capacity approximately 6.5-fold.