Jit
Enthusiast computational biologist with business dream !!!
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My commonly used commands in Bioinformatics
Last updated 2359 days ago by Rahul NayakFYI, I've found it useful to use MUMmer to extract the specific changes that Racon makes, so I can evaluate them individually: minimap -t 24 assembly.fasta long_reads.fastq.gz | racon -t 24 long_reads.fastq.gz - assembly.fasta...Referee: Genome assembly quality scores
By Jit 2258 days agogwct.github.io - Modern genome sequencing technologies provide a succint measure of quality at each position in every read, however all of this information is lost in the assembly process. Referee summarizes the quality information from the reads that map to a site...jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator
By Abhimanyu Singh 1994 days agogithub.com - jackalope simply and efficiently simulates (i) variants from reference genomes and (ii) reads from both Illumina and Pacific Biosciences (PacBio) platforms. It can either read reference genomes from FASTA files or simulate new ones. Genomic variants...Kevler: Reference-free variant discovery in large eukaryotic genomes
By Jit 1808 days agogithub.com - Welcome to kevlar, software for predicting de novo genetic variants without mapping reads to a reference genome! kevlar's k-mer abundance based method calls single nucleotide variants (SNVs), multinucleotide variants (MNVs),...sankeyNetwork with networkD3
By Jit 2470 days agochristophergandrud.github.io - You can also create Sankey diagrams with sankeyNetwork. Here is an example using downloaded JSON data: https://en.wikipedia.org/wiki/Sankey_diagramgenoPlotR - plot gene and genome maps project!
By Abhimanyu Singh 2220 days agogenoplotr.r-forge.r-project.org - genoPlotR is a R package to produce reproducible, publication-grade graphics of gene and genome maps. It allows the user to read from usual format such as protein table files and blast results, as well as home-made tabular files. Features Linear...tinycov: standalone command line utility written in python to plot coverage from a BAM file
By Jit 1753 days agogithub.com - Tinycov is a small standalone command line utility written in python to plot the coverage of a BAM file quickly. This software was inspired by Matt Edwards' genome coverage plotter. To install the stable version: pip3 install --user...Circos visualization !
By BioStar 675 days agowlcb.oit.uci.edu - Circos visualization https://wlcb.oit.uci.edu/modules/index.htmlJRF/SRF at Jawaharlal Nehru Institute ofAdvanced Studies (JNIAS), Hyderabad
Applications for Academic Projects in Biotechnology, Bioinformatics, Environmental Sciences and Computer Science & Engineering About JNIAS Jawaharlal Nehru Institute of Advanced Studies (JNIAS), Hyderabad has been established by Dr. D....Celebrating Crystallography - An animated adventure
By Jitendra Narayan 3723 days agoNEW: Now with French or Spanish subtitles (click on the 'Captions' icon to select). Plus... Watch the French language version here: https://www.youtube.com/watch?v=PvLu7BOsJhM X-ray crystallography is arguably one of the greatest innovations of the...
