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Genome in a Bottle http://jimb.stanford.edu/giab/ #GIAB #Genome

perl -pe 's/[^AGTC\n]/N/gi unless m/>/;' /media/urbe/TOSHIBALAB/falconUnzip/SSPACED_P2/scaffolds.fasta > /media/urbe/TOSHIBALAB/falconUnzip/SSPACED_P2/scaffolds_corrected.fasta #Remove #Non-ATCG

#Zero coverage regions ~/Tools/bedtools2/bin/bedtools genomecov -ibam PvsH_aln_sorted.bam -bga | awk '$4==0' > ZERO_coverage_regions.txt

Sed illegal charters from fasta. $ sed '/^[^>]/ s/[^AGTC]/N/gi' < seq.fa #fasta #otherthanATGC #replace #sed #Linux #illegal

export PERL5LIB=/home/foobar/code #SetPath #Perl

Count the contigs length in index fasta file with samtools. $ awk '{s+=$2}END{print s}' scaffolds.fasta.fai #Fasta #Index #Length #Count #Size #Samtools

Genome in a Bottle (GIAB) http://jimb.stanford.edu/giab/ #Genome #Consortium #GIAB

#Scientific #converter https://www.rapidtables.com/convert/number/scientific-notation-converter.html

ImageMagick builds on a variety of Unix and Unix-like operating systems including Linux, Solaris, FreeBSD, Mac OS X, and others.

CGView is a Java package for generating high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence annotation pipelines, as a means of generating visual output suitable for the web. Feature...

git clone https://github.com/lh3/minimap2 cd minimap2 && make # long sequences against a reference genome ./minimap2 -a test/MT-human.fa test/MT-orang.fa > test.sam # create an index first and then map ./minimap2 -d MT-human.mmi...

The Rhodes Scholarships for India Each year, there are five Scholarships available for India. https://www.rhodeshouse.ox.ac.uk/scholarships/apply/india

SWALO (scaffolding with assembly likelihood optimization) is a method for scaffolding based on likelihood of genome assemblies computed using generative models for sequencing. Please email your questions, comments, suggestions, and bug reports to...

The Malaysia International Scholarship (MIS) is an initiative by the Malaysian Government to attract the best brain from around the world to pursue advanced academic studies in Malaysia. This scholarship aims to support Malaysian Government's effort...

needleall reads a set of input sequences and compares them all to one or more sequences, writing their optimal global sequence alignments to file. It uses the Needleman-Wunsch alignment algorithm to find the optimum alignment (including gaps) of two...