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Bio-Scripts
Installing Platypus on Ubuntu !
(py27) ➜ Tools git:(master) ✗ git clo...ckerfile extensions LICENSE Makefile misc README.md release...➜ htslib-1.9 git:(master) ✗ make install zsh: correct 'instal...man/man5’: Permission denied Makefile:...are using pip version 9.0.3, however vers...rn value of ‘write’, declared with att...2031 days ago
Setting up falconUnzip conda environments for genome assembly !
➜ Analysis_Results conda create -n denovo_asm Solving environment: don...# quality that PacBio strives for, we make no w...acBio Customer Service for assistance with any #...# # We make...# # to any extent or within a...2001 days ago
- Map them agaist reference avaga genome using following codes git clone https://github.com/lh3/bwa.git cd bwa; make bwa index ref.fa bwa mem -x pacbio ref.fa pacbio.fq > aln.sam bwa mem -x ont2d ref.fa ont-2D.fq > aln.sam
1737 days ago
Install Samtools, Bcftools and htslib on Ubuntu !
#Inspired from online search sudo apt-get update sudo apt-get install gcc sudo apt-get install make sudo a...2 tar -vxjf htslib-1.9.tar.bz2 cd htslib-1.9 make...ar -vxjf samtools-1.9.tar.bz2 cd samtools-1.9 make...1570 days ago
Bash command to install bwa, samtools, picard !
(base) [wsu29@bladeamd-2 tmp]$ conda install bwa Collecting package met...2-2.9.9 | hea5a465_1 2.0 MB make-...pkgs/main/linux-64::libxml2-2.9.9-hea5a465_1 make...1567 days ago
- jit@jit-HP-Pro-3335-MT:~/Downloads/testDock$ sudo docker system df TYPE TOTAL ACTIVE SIZE RECLAIMABLE Images...
1521 days ago
- (base) jit@jit-HP-Pro-3335-MT:~/Downloads/testDock$ docker build -t autocontampr . Sending build context to Docker daemon 9.024MB Step 1/16 : FROM ubuntu:14.04 --->...
1454 days ago
Install and set up i-adhore for synteny and wgd analysis ! -- step by step --
#Need to download i-adhore-3.0.01.tar.gz from https://wdiceryfd...m_required): Compatibility with CMake < 2.8.12 will be remove...t does not need compatibility with older versions. -- The C...- found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Perform...34%] Building CXX object src/CMakeFiles/i-...1215 days ago
- vik@vik-Lenovo-ideapad-320-15ISK:~/Do...be installed: autoconf automake aut...ds autoconf-doc devscripts dh-make dwz debian-keyring g++-multil...be installed: autoconf automake auto...iously unselected package automake. Prepa...g config file /etc/R/Renviron with...-2build1) ... Setting up automake (1:...
1066 days ago
Tadpole is 250x faster than SPADes assembler !
lege@jit-Lenovo-ideapad-320-15ISK:~/Downloads/MyTools/Vir$ tadpo...=correct Extending contigs with reads could be done like this...nttodump=1 Only dump kmers with at least this depth. showstats=...inity). Memory use increases with K. pre...y base fully covered by kmers with cou...988 days ago
