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FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads
By Jit 2463 days agobioinfo.ut.ee - FastGT is a program package for whole-genome genotyping of genome variants directly from raw sequencing reads. It is written in C and runs in Linux. FastGT uses a list of variant-specific k-mer pairs that are unique in human genome, counts the...UnCoVar: Workflow for Transparent and Robust Virus Variant Calling, Genome Reconstruction and...
By BioStar 812 days agoikim-essen.github.io - UnCoVar: Workflow for Transparent and Robust Virus Variant Calling, Genome Reconstruction and Lineage Assignment Using state of the art tools, easily extended for other viruses Tool and database updates for critical components via...VG: variation graph data structures, interchange formats, alignment, genotyping, and variant...
By Jit 2463 days agogithub.com - Variation graphs provide a succinct encoding of the sequences of many genomes. A variation graph (in particular as implemented in vg) is composed of: nodes, which are labeled by sequences and ids edges, which connect two nodes via either of...Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation
By Neel 1667 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...Ensembl Variation - Calculated variant consequences
By Jit 2969 days agowww.ensembl.org - For each variant that is mapped to the reference genome, we identify all overlapping Ensembl transcripts. We then use a rule-based approach to predict the effects that each allele of the variant may have on each transcript. The set of consequence...AfterQC: Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
By Jit 3041 days ago Comments (1)github.com - Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data AfterQC can simply go through all fastq files in a folder and then output three folders: good, bad and QC folders, which contains good reads, bad reads and the QC...World of Omics
By Rahul Agarwal 4850 days ago Comments (5)How many variants of "omics" techniques presently in use ?Should you get sequenced? Not all bad genes predict disease
By Rahul Agarwal 4806 days agowww.today.com - “What we really don’t know yet is whether the predictive aspects of the genome are going to turn out to be beneficial or potentially harmful” “As we roll out genomic medicine we are fighting against this society-wide...Comparison of Short Read De Novo Alignment Algorithms
By Rahul Agarwal 4814 days agobiochem218.stanford.edu - Excellent article to introduce different sequencing methods along with tools for de novo assembly of sequencing reads and their relevant references. Title: Comparison of Short Read De Novo Alignment Algorithms Author: Nikhil GopalLatest paper on comparison of mapping tools
By Rahul Agarwal 4801 days ago Comments (1)www.biomedcentral.com - A. Hatem, D. Bozdag, A. E. Toland, U. V. Catalyurek "Benchmarking short sequence mapping tools" BMC Bioinformatics, 14(1):184, 2013. http://bmi.osu.edu/hpc/software/benchmark/ http://bmi.osu.edu/hpc/software/pmap/pmap.html Other similiar...
