Abhimanyu Singh
A bioinformatics beginner
Our Sponsors
Related items
ALPACA: A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.
By Seema Singh 2400 days agogithub.com - ALPACA requires Celera Assembler 8.3 or later. It is recommended to build Celera Assembler from source. (Why? The pre-built binaries CA_8.3rc1 and CA8.3rc2 will work for any large data set. Detail paper...Cerulean: A hybrid assembly using high throughput short and long reads
By Rahul Nayak 2364 days agosourceforge.net - Cerulean extends contigs assembled using short read datasets like Illumina paired-end reads using long reads like PacBio RS long reads. Cerulean v0.1 has been implemented with bacterial genomes in mind. The method is fully described in...ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole...
By Rahul Nayak 2336 days agogithub.com - ChopStitch is a new method for finding putative exons and constructing splice graphs using an assembled transcriptome and whole genome shotgun sequencing (WGSS) data. ChopStitch identifies exon-exon boundaries in de novo assembled RNA-seq data with...Strudel
By Anjana 2977 days agoics.hutton.ac.uk - Strudel is our graphical tool for visualizing genetic and physical maps of genomes for comparative purposes. The application aims to let the user examine their data at a variety of different levels of resolution, from entire maps to individual...FinisherSC:a repeat-aware tool for upgrading de novo assembly using long reads
By Jit 2288 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...Genome assembly forensics: finding the elusive mis-assembly
By Jit 2129 days agoamos.sourceforge.net - We present the first collection of tools aimed at automated genome assembly validation. This work formalizes several mechanisms for detecting mis-assemblies, and describes their implementation in our automated validation pipeline,...GMASS: a novel measure for genomeassembly structural similarity
By Abhimanyu Singh 2051 days agobioinfo.konkuk.ac.kr - The GMASS score is a novel measure for representing structural similarity between two assemblies. It will contribute to the understanding of assembly output and developing de novo...R Graphical Cookbook by Winston Chang
By Abhimanyu Singh 2942 days agoR Graphical Cookbook by Winston Chang A very nice book by Winston Chang for R ethusiast. The R code presented in these pages is the R code actually used to produce the Figures in the book. There will be differences compared to the code chunks shown...Free Genomics data !
By BioStar 1752 days agowww.darwintreeoflife.org - The specimens were collected by the Oxford Wytham Woods and Edinburgh Lohse lab teams. DNA extraction and sequencing was carried out by the Sanger Institute Scientific Operations teams. Assemblies were carried out by the Tree of Life team (Shane...JCVI:Python utility libraries on genome assembly, annotation and comparative genomics
By Jit 1713 days agogithub.com - Collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics. https://github.com/tanghaibao/jcvi More at https://github.com/tanghaibao/jcvi/wiki
