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Choosing the Right NGS Sequencing Instrument for Your Study
By Neel 1572 days agogenohub.com - The right sequencing instrument for your study depends on your project goal. Setting aside turnaround time and price, it essentially comes down to the numbers of reads and read length you need for your experiment. Below, we've described and compared...AIRVF: a filtering toolbox for precise variant calling in Ion Torrent sequencing
By BioStar 3208 days agosourceforge.net - AIRVF that works on flowgram, raw and mapped reads and called variants to reduce artifact-driven false variant calls. Tests on sequencing data of standard reference material showed up to ∼98% reduction of false variants when combined to...Minda: a tool for evaluating structural variant (SV) callers
By LEGE 917 days agogithub.com - Minda is a tool for evaluating structural variant (SV) callers that standardizes VCF records for compatibility with both germline and somatic SV callers, benchmarks against a single VCF input file, or benchmarks against an ensemble call set...truvari: Structural variant comparison tool for VCFs
By Jit 2286 days agogithub.com - Structural variant comparison tool for VCFs Given benchmark and comparsion sets of SVs, calculate the recall, precision, and f-measure. Spiral Genetics MotivationMIX: Combining multiple assemblies from NGS data
By Rahul Nayak 3071 days agogithub.com - Mix is a tool that combines two or more draft assemblies, without relying on a reference genome and has the goal to reduce contig fragmentation and thus speed-up genome finishing. The proposed algorithm builds an extension graph where vertices...DeepVariant : an analysis pipeline that uses a deep neural network to call genetic variants from...
By Jit 2444 days agogithub.com - DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation...Smudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data
By Neel 1682 days agogithub.com - This tool extracts heterozygous kmer pairs from kmer count databases and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovB / (CovA +...LRSDAY: Long-read Sequencing Data Analysis for Yeasts
By Poonam Mahapatra 2595 days agogithub.com - Long-read sequencing technologies have become increasingly popular in genome projects due to their strengths in resolving complex genomic regions. As a leading model organism with small genome size and great biotechnological importance, the budding...FiNGS: Filters for Next Generation Sequencing
By Neel 2045 days agogithub.com - Key features Filters SNVs from any variant caller to remove false positives Calculates metrics based on BAM files and provides filtering not possible with other tools Fully user-configurable filtering (including which filters to use and their...ngs-bits - Short-read sequencing tools
By Neel 2452 days agogithub.com - Binaries of ngs-bits are available via Bioconda. Alternatively, ngs-bits can be built from sources: Binaries for Linux/macOS From sources for Linux/macOS From sources for Windows
