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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.
fastqp Simple FASTQ quality assessment using Python. Kraken: [9] A set of tools for quality control and analysis of high-throughput sequence data. HTSeq [10] The Python script htseq-qa takes a file with sequencing reads (either raw or aligned reads) and produces a PDF file with useful plots to assess the technical quality of a run.
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.
Most high-throughput, next generation sequencing platforms produce shorter read lengths compared to Sanger sequencing.These new platforms are able to generate large quantities of data in short periods of time, but until methods were developed for de novo assembly of large genomes from short read sequences, Sanger sequencing remained the standard method of creating a reference genome. [10]
Pandas (styled as pandas) is a software library written for the Python programming language for data manipulation and analysis.In particular, it offers data structures and operations for manipulating numerical tables and time series.
This jumping library uses adaptors containing markers for fragment selection in combination with barcodes for multiplexing. The protocol was developed by Talkowski et al. [9] and based on mate-pair library preparation for SOLiD sequencing. The selected DNA fragment size is 3.5 – 4.5 kb.
scikit-learn (formerly scikits.learn and also known as sklearn) is a free and open-source machine learning library for the Python programming language. [3] It features various classification, regression and clustering algorithms including support-vector machines, random forests, gradient boosting, k-means and DBSCAN, and is designed to interoperate with the Python numerical and scientific ...
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. It was first used by Tony Cox and Zemin Ning at the Wellcome Trust Sanger Institute , and became widely known through its implementation within the SAMtools ...