Results for "Bonobo and Neandertal genome sequencing"
Bio-Scripts
Create random 2 translocations in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq simuINV.simseq.genome.fa -translocation_cou...ion simulation >> This simulation use the random seed: 1925195826 The option...= 2 [Sun Jan 10 17:12:58 2021] Introducing random Tran...1217 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_BBM...me/urbe/Tools/bbmap/current/ align2.RandomReads...sert=600 gaussian Executing align2.RandomReads3 [build=1, ref=mixed.fa,...0-0) nRate =0.0, max=0, len=(0-0) genome=1...996 days ago
Tadpole is 250x faster than SPADes assembler !
lege@jit-Lenovo-ideapad-320-15ISK:~/Downloads/MyTools/Vir$ tadp...may yield more accurate genome size estimation. contigpasse...xtend sequences to be longer, and optionally...y are very slow for large metagenomes. Overlap parameters (for...982 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-ana...
967 days ago
Installing Covid19 Environment !
(base) vikas@vikas-Lenovo-ideapad-320-15ISK:~/vinodLab/Genepi$ conda env create...one Solving environment: done Downloading and Extrac...SILVA 16S rRNA database (needed for reference genome detection in metagenomic datasets) * BUSCO tools and databa...929 days ago
Bash script to simulate a genome !
# Reference https://github.com/chhylp123/hifiasm/issues/33 #...https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/401/745/GCA_0...er.diploid.fasta.log.txt # genome size bgzip -@75 -cd GCA_0034...# make reference for randomreads.sh # randomreads.sh part.../genetics/elbers/bbmap-38.86/randomreads...923 days ago
Bash script to split multifasta file !
#Using awk, we can easily split a file (multi.fa) into chunks of size...nt >> file; }' < multi.fasta #Another great solution is genome tools (gt), which you can find here: http://genometools.org/, which has the following simple command: gt...829 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 Institute at Washington University and is hosted on github. To use Varscan...829 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...641 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-release626 days ago
