Jit
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Smudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data
By Neel 1013 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 +...lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data
By BioJoker 2199 days agogithub.com - lordFAST is a sensitive tool for mapping long reads with high error rates. lordFAST is specially designed for aligning reads from PacBio sequencing technology but provides the user the ability to change alignment parameters depending on the reads...iSeqQC: a tool for expression-based quality control in RNA sequencing
By BioStar 1753 days agogithub.com - iSeqQC, an expression-based QC tool that detects outliers either produced due to variable laboratory conditions or due to dissimilarity within a phenotypic group. iSeqQC implements various statistical approaches including unsupervised clustering,...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By BioJoker 2073 days agogithub.com - Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The...Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm
By BioStar 1724 days agogithub.com - Apollo is an assembly polishing algorithm that attempts to correct the errors in an assembly. It can take multiple set of reads in a single run and polish the assemblies of genomes of any size. Described by Firtina et al. (preliminary version...NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data
By Jit 2312 days agogithub.com - NextSV, a meta SV caller and a computational pipeline to perform SV calling from low coverage long-read sequencing data. NextSV integrates three aligners and three SV callers and generates two integrated call sets (sensitive/stringent) for different...DeepVariant : an analysis pipeline that uses a deep neural network to call genetic variants from...
By Jit 1775 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...Parliament2: Runs a combination of tools to generate structural variant calls on whole-genome...
By Jit 1651 days agogithub.com - Parliament2 identifies structural variants in a given sample relative to a reference genome. These structural variants cover large deletion events that are called as Deletions of a region, Insertions of a sequence into a region, Duplications of a...Figeno: Tool for plotting sequencing data along genomic coordinates.
By LEGE 78 days agogithub.com - Tool for plotting sequencing data along genomic coordinates. FIGENO is a FIGure GENerator for GENOmics With figeno, you can plot various types of sequencing data along genomic coordinates. Video...Indexcov: fast coverage quality control for whole-genome sequencing
By Jit 2289 days ago Comments (1)github.com - indexcov, an efficient estimator of whole-genome sequencing coverage to rapidly identify samples with aberrant coverage profiles, reveal large-scale chromosomal anomalies, recognize potential batch effects, and infer the sex of a...
