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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.
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]
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 ...
SciPy (pronounced / ˈ s aɪ p aɪ / "sigh pie" [2]) is a free and open-source Python library used for scientific computing and technical computing. [3]SciPy contains modules for optimization, linear algebra, integration, interpolation, special functions, FFT, signal and image processing, ODE solvers and other tasks common in science and engineering.
The library serves an international audience and offers books in numerous international languages. Australian Islamic Library Avalon Project: Legal studies and history: Documents in law, history and diplomacy Yale Law School [8] Baen Free Library: Science fiction and fantasy: Science fiction and fantasy from publishing house Baen Books Baen ...
Construct, a python library for the declarative construction and deconstruction of data structures; Genshi, a template engine for XML-based vocabularies; IPython, a development shell both written in and designed for Python; Jinja, a Python-powered template engine, inspired by Django's template engine; Kid, simple template engine for XML-based ...
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]