Results for "genome structure"
Bio-Scripts
Create random 5 inversions in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq simuCNV.simseq.genome.fa -inversion_count 5 -prefix simuINV [Sun Jan 10 16:30:40 2021] Starting simuG .. [Sun Jan 10 16:30:40...1254 days ago
Create random 2 translocations in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq simuINV.simseq.genome.fa -translocation_count 2 -prefix simuTRANS [Sun Jan 10 17:12:58 2021] Starting simuG .. [Sun Jan 10 17...1253 days ago
Commandline for paired end reads simulation with BBMap !
(JitMetaENV) ➜ mixedSample git:(main) ✗ /home/urbe/Tools/bbmap/randomreads.sh ref=mixed.fa out=reads_BBMAP250.fq...x=0, len=(0-0) subRate=0.0, max=0, len=(0-0) nRate =0.0, max=0, len=(0-0) genome=1...1033 days ago
Tadpole is 250x faster than SPADes assembler !
lege@jit-Lenovo-ideapad-320-15ISK:~/Downloads/MyTools/Vir$ tadpole.sh...mmended that mce=1 for low-depth metagenomes. mincountretain=0 (mincr...may yield more accurate genome size estimation. contigpasse...but they are very slow for large metagenomes....1019 days ago
- #Create a conda environment. #Install a Python package in the terminal using conda. $ conda create -n myenv...env update -f environment.yml #Adding a Package to your YAML File name: genome-an...
1004 days ago
Installing Covid19 Environment !
(base) vikas@vikas-Lenovo-ideapad-320-15ISK:~/vinodLab/Genepi$ conda env create -f covid19-environment.yml Collec...ructural variants detection) * SILVA 16S rRNA database (needed for reference genome de...966 days ago
Bash script to simulate a genome !
# Reference https://github.com/chhylp123/hifiasm/issues/33 # Use Drosophila melongas...lbers/test/fly2 wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/401/745/GCA_0034...174v1_genomic.fna_upper.diploid.fasta.log.txt # genome si...960 days ago
Bash script to split multifasta file !
#Using awk, we can easily split a file (multi.fa) into chunks of size N (here, N=500), by using the fo...} { print >> file; }' < multi.fasta #Another great solution is genome tools (gt), which you can find here: http://genometoo...866 days ago
Install Varscan on Ubuntu / Linux !
#Varscan is a java program designed to call variants in sequencing data. It was developed at the Genome In...866 days ago
Script to rapid genome clustering based on pairwise ANI
First, create a blast+ database: makeblastdb -in -dbtype nucl -out Next, use megablast from blast+ package to perform all-vs-all blastn of sequences: blastn -query...678 days ago
