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Bio-Scripts
# Make sure that Java v8+ is installed: java -version # Install Nextflow curl -fsSL get.nextflow.io | bash # Add Nextflow binary to your PATH: mv nextflow ~/bin/ # OR system-wide installation: # sudo mv nextflow /usr/local/bin974 days ago
Downloading mmseqs databases !
# mmseqs databases Usage: mmseqs databases [options] Name Type Tax...- https://pfam.xfam.org - Pfam-B Profile - https://xfam.wordpres...954 days ago
- # make reference for randomreads.sh # randomreads.sh part of BBTools/BB...th=100000 \ out=/dev/null # make 60x...rGenie 1.7051 to get an idea of k-mer with that pr...\d+"` echo "best k=${k}" # make...random_reads_pacbio.log 2>&1 # make 30x...
940 days ago
Installing Covid19 Environment !
(base) vikas@vikas-Lenovo-ideapad-320-15ISK:~/vinodLab/Genepi$ conda env...################################################## | 100% make-...nomic data stored elsewhere, simply replace this directory with a s...935 days ago
Bash script to simulate a genome !
# Reference https://github.com/chhylp123/hifiasm/issues/33 #...per-case bases, also compress with bgzip # https://github.com/l...# Convert to diploid with approximately 2% heterozygosi...135 # 2% heterozygosity is how many...aplotype0.fasta.gz # make referen...929 days ago
Install Install Gffcompare on Ubuntu / Linux
#Gffcompare is a program that is used to perform operatio...files. It has a binary distribution compatible with the lin...re using so we will just download, extract, and make...-xzvf gffcompare-0.9.8.Linux_x86_64.tar.gz # make sym...835 days ago
- #R is a feature rich interpretive progra...we’d configure the installation with --with-x=no which tells R to install...nload later. From there we’d do make and make inst...e commented out the code below, however it i...ix=/home/ubuntu/workspace/bin --with-x=no make make install ## make sym...
835 days ago
Install StringTie on ubuntu / Linux !
#StringTie is a software program to perform transcript assembly and quantification...o to install we can just download this distribution and extract it. Like with our other programs we also make a symlink to make it...835 days ago
- #GATK is a toolkit developed by the broad institute focused prima...y using the yaml file included within GATK as the instructions fo...irtual environment. We do this with the...should be stored. We will also make a symli...p unzip gatk-4.0.2.1.zip # make...own conda environments sudo chown -R...
823 days ago
Genome Scaffolding and gap filling !
scaffolding with ARCS v1.0.3 (−c3, −l,4, −a,0.9, −z500, −m50, −20 000, −e30000, −s90). https://github.com/bcgsc/arcs Next, automated gap filling was performed using Sealer v2.0.1 (−L150, -P10, −k75-115 [step = 10]) https://github.com/bcgsc/abyss/tree/sealer-release632 days ago
