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

RepeatModeler2 represents a valuable addition to the genome annotation toolkit that will enhance the identification and study of TEs in eukaryotic genome sequences. RepeatModeler2 is available as source code or a containerized package under an open...

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

Simulated genomes with pre-defined and random genomic variants can be very useful for benchmarking genomic and bioinformatics analyses. Here we introduce simuG, a lightweight tool for simulating the full-spectrum of genomic variants (single...

The Environment for Tree Exploration (ETE) is a Python programming toolkit that assists in the recontruction, manipulation, analysis and visualization of phylogenetic trees (although clustering trees or any other tree-like data structure are also...

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))}'

You need to add this file https://bioinformaticsonline.com/file/view/36952/getoptspl-file at requested location. Cheers

Cannot locate getopts.pl 

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

Interactive Periodic Table of the Elements, in Pictures and Words This periodic table is easy to remember https://elements.wlonk.com/ElementsTable.htm 

  Seq is a programming language for computational genomics and bioinformatics. With a Python-compatible syntax and a host of domain-specific features and optimizations, Seq makes writing high-performance genomics software as easy as writing...

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