BioStar
Bioinformatician
Our Sponsors
Related items
EXCAVATOR: detecting copy number variants from whole-exome sequencing data
By Radha Agarkar 2618 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...Ktrim: an extra-fast and accurate adapter- and quality-trimmer for sequencing data
By Jit 1849 days agogithub.com - Ktrim is written in C++ for GNU Linux/Unix platforms. After uncompressing the source package, you can find an executable file ktrim under bin/ directory compiled using g++ v4.8.5 and linked with libz...SimLoRD: A read simulator for third generation sequencing reads
By Aaryan Lokwani 2753 days agobitbucket.org - SimLoRD is a read simulator for third generation sequencing reads and is currently focused on the Pacific Biosciences SMRT error model. Reads are simulated from both strands of a provided or randomly generated reference sequence. The reference...HASLR: a hybrid assembler which uses both second and third generation sequencing reads
By BioStar 2132 days agogithub.com - HASLR, a hybrid assembler which uses both second and third generation sequencing reads to efficiently generate accurate genome assemblies. Our experiments show that HASLR is not only the fastest assembler but also the one with the lowest number of...NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data
By Jit 2769 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 2232 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 2108 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...Smudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data
By Neel 1470 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 2384 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...poRe: an R package for the visualization and analysis of nanopore sequencing data
By Jit 3025 days ago Comments (1)academic.oup.com - Motivation: The Oxford Nanopore MinION device represents a unique sequencing technology. As a mobile sequencing device powered by the USB port of a laptop, the MinION has huge potential applications. To enable these applications, the...
