Jit
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PureCN: copy number calling and SNV classification using targeted short read sequencing
By Jit 2767 days agobioconductor.org - This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with...QuasR: Quantification and annotation of short reads in R
By Neel 1667 days agowww.bioconductor.org - The QuasR package (short for Quantify and annotate short reads in R) integrates the functionality of several R packages (such as IRanges (Lawrence et al. 2013) and Rsamtools) and external software (e.g. bowtie, through the Rbowtie package, and...DAVI: Deep learning-based tool for alignment and single nucleotide variant identification
By Jit 1817 days ago Comments (1)github.com - DAVI consists of models for both global and local alignment and for variant calling. We have evaluated the performance of DAVI against existing state-of-the-art tool sets and found that its accuracy and performance is comparable to existing tools...MAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data
By BioStar 1927 days agogithub.com - The algorithm presented herein, Mining Algorithm for GenetIc Controllers (MAGIC), uses ENCODE ChIP-seq data to look for statistical enrichment of TFs and cofactors in gene bodies and flanking regions in gene lists without...LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data
By Neel 1718 days ago Comments (1)academic.oup.com - LoReTTA (Long Read Template-Targeted Assembler), a tool designed for performing de novo assembly of long reads generated from viral genomes on the PacBio platform. LoReTTA exploits a reference genome to guide the assembly process, an approach that...Smudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data
By Neel 1471 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 2385 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...AIRVF: a filtering toolbox for precise variant calling in Ion Torrent sequencing
By BioStar 2997 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...iSeqQC: a tool for expression-based quality control in RNA sequencing
By BioStar 2211 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,...TAREAN: A computational tool for identification and characterization of satellite DNA from...
By Surabhi Chaudhary 2853 days agobitbucket.org - TAndem REpeat ANalyzer -TAREAN – is a computational pipeline for unsupervised identification of satellite repeats from unassembled sequence reads. The pipeline uses low-pass whole genome sequence reads and performs their...
