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QuasR: Quantification and annotation of short reads in R
By Neel 1198 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...Figeno: Tool for plotting sequencing data along genomic coordinates.
By LEGE 67 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...Circleator
By Jit 2708 days agogithub.com - The Charm City Circleator--or Circleator for short--is a Perl-based visualization tool developed at the Institute for Genome Sciences in the University of Maryland's School of Medicine. Circleator produces circular plots of...PLAST: A fast, accurate and NGS scalable bank-to-bank sequence similarity search tool
By Jit 2549 days agohttps://plast.inria.fr/ - PLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of seeds-based heuristic comparison methods, such as the Blast suite of algorithms. Relying on unique software architecture,...CAMSA :: a tool for Comparative Analysis and Merging of Scaffold Assemblies
By Rahul Nayak 2522 days agohttps://cblab.org/camsa/ - CAMSA – is a tool for Comparative Analysis and Merging of Scaffold Assemblies, distributed both as a standalone software package and as Python library under the MIT license. Main features: works with any number of...%MinMax: A versatile tool for calculating and comparing synonymous codon usage and its impact on...
By Surabhi Chaudhary 2375 days agohttp://www.codons.org/ - %MM calculates whether a given gene sequence encodes amino acids using the most common codons possible, the least common codons possible, or (most typically) some combination of these extremes. See our PLoS ONE paper for more details on how the...“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
By Poonam Mahapatra 2364 days agodoua.prabi.fr - One code to find them all is a set of perl scripts to extract useful information from RepeatMasker about transposable elements, retrieve their sequences and get some quantitative information. Assemble RepeatMasker hits into complete TE copies,...LSC :a long read error correction tool
By Jit 2305 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...FinisherSC:a repeat-aware tool for upgrading de novo assembly using long reads
By Jit 2287 days agogithub.com - Here is the command to run the tool: python finisherSC.py destinedFolder mummerPath If you are running on server computer and would like to use multiple threads, then the following commands can generate 20 threads to run FinisherSC. python...rHAT: a seed-and-extension-based noisy long read alignment tool
By Abhimanyu Singh 2253 days agogithub.com - rHAT is a seed-and-extension-based noisy long read alignment tool. It is suitable for aligning 3rd generation sequencing reads which are in large read length with relatively high error rate, especially Pacbio's Single Molecule Read-time (SMRT)...
