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

  • Install Packages in Python

    #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