List of tools frequently used while genome assembly
...genome assembly characteristics ANI.pl (https://github.com/chjp/ANI) CheckM (v. 1.0.7) Prokka (v. 1.12) QUAST (v. 2.3) mummer (v. not available) If...1983 days ago
Software for genome assembly !
...ab.org/ 10 Bandage graph assembly viewer https://rrwick.github.io/Bandage/ 11 Gepard dotter http://cube.univie.ac.at/gepard 12 MUMmer aligner and plotter http://mummer.sourceforge.net/1397 days ago
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Useful Publications and Websites for Deep Sequencing Data Analysis
...ariant detection Versatile and open software for comparing large genomes. Kurtz et al, Genome Biol (5(2):R12, 2004. PubMedCentral [describes the MUMmer software for full-genome alig...3833 days ago
Install Nucmer on Linux / Ubuntu
...oads/MitoHunter$ sudo apt install mummer [sudo] password for jit: R...ckages will be installed: gawk mummer 0 upgraded, 2 newly installe....com/ubuntu bionic/universe amd64 mummer amd64 3.23+dfsg-3 [811 kB] F...3+dfsg-3_amd64.deb ... Unpacking mummer (3.23+dfsg-3) ... Setting up...1603 days ago
Bash script to check installed bioinformatics program !
allTools=(bwa mummer trimomatic) decFlag=0; for name in ${allTools[@]}; do #echo "enter your package name" # read name dpkg -s $name &> /dev/null if [ $...1099 days ago
dotPlotly: Generate an interactive dot plot from mummer or minimap alignments
Create an interactive dot plot from mummer output OR PAF format R script that makes a plotly interactive and/or static (png/pdf) dot plot. Shiny app available for testingTags: dotPlotly, Generate, interactive, dot, plot, mummer, minimap, alignments
1953 days ago
Tags: MUM&Co, simple, bash, script, Whole, Genome, Alignment, information, MUMmer, detect, variants
792 days ago
Comment on "SPAdes hybrid genome assembly"
...Finally, a quick comparison to the reference: sudo apt-get install mummer curl -s "http://eutils.ncbi...tmode=txt" > NC_000913.3.fa nucmer NC_000913.3.fa single_contig.fa mummerplot -png out.delta display o...2227 days ago