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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

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

mosdepth can output: per-base depth about 2x as fast samtools depth--about 25 minutes of CPU time for a 30X genome.mean per-window depth given a window size--as would be used for CNV calling.the mean per-region given a BED file of regions.a...

Learn More about  Computer Aided Drug Designing (CADD)!!! #rasalsi #rasa In our Industrial program you will get Knowledge on RNA Seq, CHIP Seq, Batch Starts From 18th November 2019 #hurryup #registernow #enquirenow The primary goal of the...

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