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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.
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 ...
Paired-end and long-read sequencing of the same sample can mitigate the deficits in short read sequencing by serving as a template or skeleton. Metrics to assess the quality of a de novo assembly include median contig length, number of contigs and N50. [66] RNA-Seq alignment with intron-split short reads.
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]
SOAP: robust with a small (1-3) number of gaps and mismatches. Speed improvement over BLAT, uses a 12 letter hash table. SOAP2: using bidirectional BWT to build the index of reference, and it is much faster than the first version. SOAP3: GPU-accelerated version that could find all 4-mismatch alignments in tens of seconds per one million reads.
Converts measurements to other units. Template parameters [Edit template data] This template prefers inline formatting of parameters. Parameter Description Type Status Value 1 The value to convert. Number required From unit 2 The unit for the provided value. Suggested values km2 m2 cm2 mm2 ha sqmi acre sqyd sqft sqin km m cm mm mi yd ft in kg g mg lb oz m/s km/h mph K C F m3 cm3 mm3 L mL cuft ...
Template to convert other currencies into United States dollars, by year, based on information from the International Monetary Fund, and with selected number of significant figures Template parameters Parameter Description Type Status amount 1 value in foreign currency to convert to USD Example 175000 Number required country code 2 country ISO 3166-1 alpha-3 country code Example MEX Line ...
Genome size ranges (in base pairs) of various life forms. Genome size is the total amount of DNA contained within one copy of a single complete genome.It is typically measured in terms of mass in picograms (trillionths or 10 −12 of a gram, abbreviated pg) or less frequently in daltons, or as the total number of nucleotide base pairs, usually in megabases (millions of base pairs, abbreviated ...