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Figeno: Tool for plotting sequencing data along genomic coordinates.
By LEGE 768 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...Finding the Hidden Switches: The Story of KiNext and Protein Kinases
By LEGE 31 days agoEvery newly sequenced genome contains thousands of proteins, but identifying what each protein does is a much harder task. Among these proteins are protein kinases, important molecular regulators that control processes such as cell growth,...EXCAVATOR2tool
By Bulbul 3616 days agosourceforge.net - EXCAVATOR2 is a collection of bash, R and Fortran scripts and codes that analyses Whole Exome Sequencing (WES) data to identify CNVs. EXCAVATOR2 enhances the identification of all genomic CNVs, both overlapping and non-overlapping targeted exons by...Mulan: MUltiple sequence Local AligNment and conservation visualization tool
By Rahul Nayak 3384 days agomulan.dcode.org - Mulan performs multiple (2 or more) sequence alignments with an efficient and rapid "full local" alignment strategy that ensures a recapitulation of evolutionary sequence rearrangements (such as inversions and reshuffling) in any of the species. It...COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
By Jit 3245 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...Synima: Synteny Imaging tool
By Jit 3241 days agogithub.com - Synteny Imaging tool (Synima) written in Perl, which uses the graphical features of R. Synima takes orthologues computed from reciprocal best BLAST hits or OrthoMCL, and DAGchainer, and outputs an overview of genome-wide synteny in PDF. Each of...Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput...
By Jit 3111 days agogithub.com - Heap, that enables robustly sensitive and accurate calling of SNPs, particularly with a low coverage NGS data, which must be aligned to the reference genome sequences in advance. To reduce false positive SNPs, Heap determines genotypes and calls...Porechop: tool for finding and removing adapters from Oxford Nanopore reads
By Rahul Nayak 3071 days agogithub.com - Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop...D-GENIES: A tool for Dotplot large Genomes in an Interactive, Efficient and Simple way
By Jit 3058 days agodgenies.toulouse.inra.fr - D-GENIES – for Dotplot large Genomes in an Interactive, Efficient and Simple way – is an online tool designed to compare two genomes. It supports large genome and you can interact with the dot plot to improve the visualisation. We use minimap...LSC :a long read error correction tool
By Jit 3006 days agowww.healthcare.uiowa.edu - Getting Started These simple steps will help you integrate LSC into your transcriptomics analysis pipeline. Read the LSC_requirements for running LSC. Download and set-up the LSC package. Follow the tutorial to see how...
