NGS Software

1. FASTX Tool Kit

   :The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

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2. The Genome Analysis Toolkit (GATK)

   :The GATK is a structured software library that makes writing efficient analysis tools using next-generation sequencing data very easy, and second it’s a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner.

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3. Burrows Wheeler Algorithm Download

   :"BWA is a program for aligning sequencing reads against a large reference genome (e.g. human genome). It has two major components, one for read shorter than 150bp and the other for longer reads".

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4. SAM Tools

   :"SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format".

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5. BFAST

   :BFAST stands for "Blat-like Fast Accurate Search Tool ". "BFAST facilitates the fast and accurate mapping of short reads to reference sequences ".

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6. BWA

   :"BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for Illumina sequence reads up to 100bp, while the rest two for longer sequences ranged from 70bp to 1Mbp "

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7. Bowtie

   :"Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small"

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8. VariationHunter

   :"VariationHunter-CommonLaw is a tool for discovery of structural variation in one or more individuals simultaneously using high throughput technologies"

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9. 9.mrFast

   :It is Micro Read Fast Alignment Search Tool. This tool is "designed to map short reads generated with the Illumina platform to reference genome assemblies; in a fast and memory-efficient manner"

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10. 10.SOAP Aligner

    :"It is an updated version of SOAP software for short oligonucleotide alignment. The new program features in super fast and accurate alignment for huge amounts of short reads generated by Illumina/Solexa Genome Analyzer"

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Bioinformatics MCQs