Jit
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RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes
By Rahul Nayak 2136 days agogithub.com - RefKA, a reference-based approach for long read genome assembly. This approach relies on breaking up a closely related reference genome into bins, aligning k-mers unique to each bin with PacBio reads, and then assembling each bin in parallel...MMseqs2: ultra fast and sensitive sequence search and clustering suite
By Abhi 1613 days agogithub.com - MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin)...Termal: a fast and interactive terminal-based viewer for multiple sequence alignments
By LEGE 166 days agogithub.com - termal, a fast, interactive, terminal-based viewer for multiple sequence alignments (MSAs), designed for use on remote systems such as high-performance computing (HPC)...RAINBOWR: Reliable Association INference By Optimizing Weights with R (R package for SNP-set GWAS...
By Surabhi Chaudhary 2198 days agogithub.com - RAINBOWR(Reliable Association INference By Optimizing Weights with R) is a package to perform several types of GWAS as follows. Single-SNP GWAS with RGWAS.normal function SNP-set (or gene set) GWAS with RGWAS.multisnp function (which tests...ClipCrop: a tool for detecting structural variations with single-base resolution using...
By BioJoker 2603 days agogithub.com - ClipCrop for detecting SVs with single-base resolution using soft-clipping information. A soft-clipped sequence is an unmatched fragment in a partially mapped read. To assess the performance of ClipCrop with other SV-detecting tools, we generated...COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
By Jit 3013 days agoftp.genomics.org.cn - An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE...Troyanskaya Lab
The goal of our research is to interpret and distill this complexity through accurate analysis and modeling of molecular pathways, particularly those in which malfunctions lead to the manifestation of disease. We are inventing integrative methods...Liftoff: an accurate tool that maps annotations in GFF or GTF between assemblies
By Jit 2076 days agogithub.com - Liftoff, an accurate tool that maps annotations in GFF or GTF between assemblies of the same, or closely-related species. Unlike current coordinate lift-over tools which require a pre-generated “chain” file as input, Liftoff is a...karyoploteR: plot whole genomes with arbitrary data
By Abhimanyu Singh 2955 days agobernatgel.github.io - karyoploteR is an R package to create karyoplots, that is, representations of whole genomes with arbitrary data plotted on them. It is inspired by the R base graphics system and does not depend on other graphics packages. The aim of karyoploteR...Scripts for the analysis of HGT in genome sequence data.
By Jit 3020 days agogithub.com - Scripts for the analysis of HGT in genome sequence data
