BOL

https://github.com/crazyhottommy/getting-started-with-genomics-tools-and-resources/blob/master/Next%20Generation%20Sequencing%20spreadsheet%20-%20T.tsv #NGS #CheatSheet

#BlobToolKit can be used during #assembly to filter non-target DNA, helping researchers produce assemblies with high biological credibility. https://blobtoolkit.genomehubs.org/view #Genome #Blob #Con

Perl script to run in parallel https://perlmaven.com/speed-up-calculation-by-running-in-parallel #Perl #Parallel #Script #Core #Thread

Perl onliner to add string to each of the fasta header. $ perl -p -e 's/^(>.*)$/$1-origin/g' in.fasta > out.fasta #String #Header #Fasta

Multifasta 2 singlefasta cat toy.fasta| awk '{ if (substr($0, 1, 1)==">" {filename=(substr($0,2) ".fa")} print $0 > filename }' #Split #fasta #multifasta

One can evaluate the accuracy of a mapper or a SNP caller with wgsim_eval.pl that comes with the package. #Evaluate #Mapping #SNP

Deep_learning course https://www.slideshare.net/TessFerrandez/notes-from-coursera-deep-learning-courses-by-andrew-ng #AI #DeepLearn

Multiline to singleline covert. $ awk '/^>/ {printf("%s%s\t",(N>0?"\n":""),$0);N++;next;} {printf("%s",$0);} END {printf("\n");}' < input.fa #Multi #Single #Convert #awk

#Estimate the #insert #size with mapped reads $ head -10000 mappings.sam | awk '{ if ($9 > 0) { N+=1; S+=$9; S2+=$9*$9 }} END { M=S/N; print "n="N", mean="M", stdev="sqrt ((S2-M*M*N)/(N-1))}'

Graph reference genome https://vimeo.com/184983995 #Graph #Reference #Genome #GraphRef

This works and I dont know how :) perl -pe '}{$_=$.' filename #Perl #Magic #PerlMagic

https://www.frontiersin.org/articles/10.3389/fmicb.2018.00973/full #Recent #HGT

Kill the screen $ screen -X -S [session # you want to kill] quit #Screen #Quit #Linux #Session #Remote

#Rename the #fasta #header and #keep first $ perl -ne 'if (/^(>\S+)/){print "$1\n";}else{print $_;}' realTestDATA.fa > realTestDATA_headerCorrected.fa #Perl

R versus Python language https://data-flair.training/blogs/r-vs-python/ #R #Python