Results for "Whole genome re-sequencing"
Bio-Scripts
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 17:1...1221 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...=0, len=(0-0) subRate=0.0, max=0, len=(0-0) nRate =0.0, max=0, len=(0-0) genome=1 PER...1000 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. O...986 days ago
- #Create a conda environment. #Install a Python package in the terminal using conda. $ conda create -n myenv...nv update -f environment.yml #Adding a Package to your YAML File name: genome-analyt...
971 days ago
Installing Covid19 Environment !
(base) vikas@vikas-Lenovo-ideapad-320-15ISK:~/vinodLab/Genepi$ conda env create -f covid19-environment.yml Colle...uctural variants detection) * SILVA 16S rRNA database (needed for reference genome detect...933 days ago
Bash script to simulate a genome !
# Reference https://github.com/chhylp123/hifiasm/issues/33 # Use Drosophila melonga...bers/test/fly2 wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/401/745/GCA_0034...74v1_genomic.fna_upper.diploid.fasta.log.txt # genome size...928 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 f...{ print >> file; }' < multi.fasta #Another great solution is genome tools (gt), which you can find here: http://genometools.o...833 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 Instit...833 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 -...645 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-release630 days ago
