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Short-read assembly using Spades !
Last updated 1027 days ago by Abhimanyu Singh Comments (2)If we only had Illumina reads, we could also assemble these using the tool Spades. You can try this here, or try it later on your own data. Get data We will use the same Illumina data as we used above: illumina_R1.fastq.gz: the Illumina...-
Mitochondrial genome assembly tools !
Last updated 445 days ago by AbhiMitochondrial genome assembly tools are specialized software and algorithms designed to accurately reconstruct the mitochondrial genome (mitogenome) from sequencing data, typically obtained through techniques like next-generation sequencing (NGS).... Resolving the complexity of the human genome using single-molecule sequencing
By Rahul Agarwal 3423 days agowww.nature.com - The human genome is arguably the most complete mammalian reference assembly yet more than 160 euchromatic gaps remain and aspects of its structural variation remain poorly understood ten years after its completion. The results in this paper...EXCAVATOR: detecting copy number variants from whole-exome sequencing data
By Radha Agarkar 2150 days agosourceforge.net - EXCAVATOR, for the detection of copy number variants (CNVs) from whole-exome sequencing data. EXCAVATOR combines a three-step normalization procedure with a novel heterogeneous hidden Markov model algorithm and a calling method that classifies...vt: a variant tool set that discovers short variants from Next Generation Sequencing data.
By Jit 1761 days agogenome.sph.umich.edu - vt is a variant tool set that discovers short variants from Next Generation Sequencing data. https://genome.sph.umich.edu/wiki/Vt https://github.com/atks/vtJASMINE: Jointly Accurate Sv Merging with Intersample Network Edges
By Shruti Paniwala 875 days agogithub.com - This tool is used to merge structural variants (SVs) across samples. Each sample has a number of SV calls, consisting of position information (chromosome, start, end, length), type and strand information, and a number of other values. Jasmine...LRCstats: a tool for evaluating long reads correction methods
By Aaryan Lokwani 2285 days agogithub.com - LRCstats is an open-source pipeline for benchmarking DNA long read correction algorithms for long reads outputted by third generation sequencing technology such as machines produced by Pacific Biosciences. The reads produced by third generation...Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation
By Neel 965 days agogithub.com - Merfin, a k-mer based variant-filtering algorithm for improved accuracy in genotyping and genome assembly polishing. Merfin evaluates each variant based on the expected k-mer multiplicity in the reads, independently of the quality of the...gEVAL: Genome Evaluation Browser
By Jit 1985 days agogeval.sanger.ac.uk - The gEVAL Browser allows the evaluation of genome assemblies through its tools and pre-computed analyses. The strength of this browser is the ability to navigate an up to date assembly and identify problematic regions and assist in...
