Results for "Linux"

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  • Linux for bioinformatician !!!

    Linux, free operating system for computers,...d of bioinformatics relies heavily on Linux-based computers and software....basic admin tasks. The focus of this linux series is to help you underst...read this article "An introduction to Linux for bioinformatics" by Paul S...

    1412 days ago

  • Subprocess pkg

    Subprocess is one of simplest way of running linux command from within python code Example: if you want to run fastqc for QC of fastq file: from subprocess import Popen,PIPE,call...

    1256 days ago

  • Tool: Gene Set Clustering based on Functional annotation (GeneSCF)

    ...durilab.org/   Requirement:   GeneSCF only works on Linux system, it has been successfully tested on Ubuntu, Mint and Cent OS. Other distributions of Linux might work as well.  ...

    578 days ago

  • A guide for complete R beginners !

    ...eblog.org/wp-content/uploads/bioinf/kerr/data.tsv Start R (type R on a Linux or Mac terminal, or find the...ful if it is also the directory where your input data is stored. Mac/Linux: this is the directory where...

    1068 days ago

  • Cheatsheet for Linux !!

    Linux Commands Cheat Sheet    File System    ls — list items in current directory    ls -l — list items in cur...

    581 days ago

  • SLURM basics !

    SLURM is a queue management system and stands for Simple Linux Utility for Resource Management. SLURM was developed at the Lawrence Livermore National Lab and currently runs some of...

    621 days ago

  • My most common one-liner in bioinformatics

    ...filecat reads.fastq | awk '{if(NR%4==2) print length($1)}' | sort -n | uniq -c > read_length.txt Plot syntenty /home/urbe/Tools/Sibelia-3.0.6-Linux/bin/Sibelia -s far --gff -q -...

    8 hours ago

  • Software packages for next gen sequence analysis

    ...n Langmead and Cole Trapnell. Linux, Windows, and Mac OS X. * BWA...;mberg at Boston College. Win/Linux/MacOSX * MrFAST and MrsFAST -...x and James Mullikin. C++ for Linux/Alpha. * SOCS - Aligns SOLiD...d Perl-CGI web-based frontend/Linux. * STADEN - Includes GAP4. G...

    949 days ago

  • SPAdes hybrid genome assembly

    ...unning spades.py will show you the options: spades.py This produces: SPAdes genome assembler v3.10.1 Usage: /usr/local/SPAdes-3.10.1-Linux/bin/spades.py [options] -o &l...

    58 days ago

  • Commercial and public next-gen-seq (NGS) software

    ...Commercial. Windows, Mac OS X and Linux.Galaxy - Galaxy = interactive...by Ben Langmead and Cole Trapnell. Linux, Windows, and Mac OS X. BWA -...ömberg at Boston College. Win/Linux/MacOSX MrFAST and MrsFAST - m...lli, M. Osteras, and J. Schrenzel. Linux/Win. EULER-SR - Short read de...

    1225 days ago