BOL

Ten steps to get started in #Genome #Assembly and #Annotation https://f1000research.com/articles/7-148/v1

Estimate the genome size https://bioinformatics.uconn.edu/genome-size-estimation-tutorial/ #Genome #Size #Estimate

http://www.iprotein.info/ #genome #pathways #visualisation

Why are de Bruijn #graphs useful for #genome #assembly? https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5531759/

Convert masked genome to N letters. $ perl -pe '/^[^>]/ and $_=~ s/[a-z]/N/g' genomic.fna > genomic.N-masked.fna #Genome #Masked #N #Convert

Unmasking the lower case values in genome. $ perl -pe '/^[^>]/ and $_=uc' genomic.fna > genomic.unmasked.fna #Genome #Unmask #Perl #Oneliner

#Genome #submission to #GenBank https://www.ncbi.nlm.nih.gov/genbank/genomesubmit/

Plotting alignment genome.crg.es/software/gfftools/GFF2APLOT.html #Alignment #Plot #Genome #gff #gfftools

Steps for #Prokaryotic #genome #assembly and #annotation http://www.edamamecourse.org/docs/metagenome_assembly_and_annotation.html

AVID: A Global Alignment Program https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430967/ #AVID #Alignment #Global #Sequence #Genome

Basics for assembly http://ged.msu.edu/angus/files/lecture4-mapping.pdf #Genome #Mapping #Assembly #PPT

Mammalian Meiotic Recombination: A Toolbox for Genome Evolution http://www.karger.com/Article/FullText/452822 #Mammals #Genome #Breakpoints #Evolution #Recombination

Genome and coverage https://rtsf.natsci.msu.edu/_rtsf/assets/File/depth%20and%20coverage.pdf #Coverage #Genome #Depth #Reads #NGS

Coverage R Plot http://davetang.org/muse/2013/09/07/creating-a-coverage-plot-in-r/ #R #Plot #Genome #Image #NGS #BAM

Understanding N50 http://jermdemo.blogspot.be/2008/11/calculating-n50-from-velvet-output.html #N50 #Assembly #Genome #Contigs