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LSC :a long read error correction tool
By Jit 2335 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...LRCstats: a tool for evaluating long reads correction methods
By Aaryan Lokwani 2315 days agogithub.com - LRCstats is an open-source pipeline for benchmarking DNA long read correction algorithms for long reads outputted by third generation sequencing technology such as machines produced by Pacific Biosciences. The reads produced by third generation...GRSR: a tool for deriving genome rearrangement scenarios from multiple unichromosomal genome...
By Jit 2278 days agogithub.com - GRSR is a Tool for Deriving Genome Rearrangement Scenarios for Multiple Uni-chromosomal Genomes. This tool will do the following steps: Step 1. Run mugsy to get multiple sequence alignment results. Step 2 & 3. Extraction of the Coordinates...KOALA: KEGG's internal annotation tool for K number assignment of KEGG GENES using SSEARCH...
By Abhimanyu Singh 2203 days agowww.kegg.jp - KOALA (KEGG Orthology And Links Annotation) is KEGG's internal annotation tool for K number assignment of KEGG GENES using SSEARCH computation. BlastKOALA and GhostKOALA assign K numbers to the user's sequence data...Minipolish: A tool for Racon polishing of miniasm assemblies
By BioStar 1847 days agogithub.com - Miniasm is a great long-read assembly tool: straight-forward, effective and very fast. However, it does not include a polishing step, so its assemblies have a high error rate – they are essentially made of stitched-together pieces of long...HASLR: a tool for rapid genome assembly of long sequencing reads
By LEGE 1788 days agogithub.com - HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which means it requires long reads generated by Third Generation Sequencing technologies (such as PacBio or Oxford Nanopore) together with Next Generation...mixtureS: a novel tool for bacterial strain reconstruction from reads
By BioStar 1585 days agowww.cs.ucf.edu - mixtureS that can de novo identify bacterial strains from shotgun reads of a clonal or metagenomic sample, without prior knowledge about the strains and their variations. Tested on 243 simulated datasets and 195 experimental datasets, mixtureS...MAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data
By BioStar 1488 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...Comparative genomics visualisation tools !
By Neel 1040 days agocmdcolin.github.io - Comparative genomics visualisation tools !Alvis: a tool for contig and read ALignment VISualisation and chimera detection
By LEGE 229 days agogithub.com - Alvis, a simple command line tool that can generate visualisations for a number of common alignment analysis tasks. Alvis is a fast and portable tool that accepts input in a variety of alignment formats and will output production ready vector...
