Results for "genome letters"
Bio-Scripts
Create random 1000 INDEL in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq simuSNP.simseq.genome.fa -indel_count 1000 -prefix simuINDEL [Sun Jan 10 16:14:00 2021] Starting simuG .. [Sun Jan 10 16:14:...1212 days ago
Create random 1000 CNVs in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq simuINDEL.simseq.genome.fa -cnv_count 100 -prefix simuCNV [Sun Jan 10 16:24:20 2021] Starting simuG .. [Sun Jan 10 16:24:20 2...1212 days ago
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 16:30:4...1212 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 1...1212 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 p...ax=0, len=(0-0) subRate=0.0, max=0, len=(0-0) nRate =0.0, max=0, len=(0-0) genome=...991 days ago
Tadpole is 250x faster than SPADes assembler !
lege@jit-Lenovo-ideapad-320-15ISK:~/Downloads/MyTools/Vir$ tadpole.sh...ommended 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...977 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-...
962 days ago
Perl script for Smith-Waterman Algorithm
# Smith-Waterman Algorithm # usage statement die "usage: $0 \n" unl..., $seq2) = @ARGV; # scoring scheme my $MATCH = 1; # +1 for letters that match my $MISMATCH = -1; # -1 for letters that mismatch my $GAP =...951 days ago
Installing Covid19 Environment !
(base) vikas@vikas-Lenovo-ideapad-320-15ISK:~/vinodLab/Genepi$ conda env create -f covid19-environment.yml Collect...tructural variants detection) * SILVA 16S rRNA database (needed for reference genome...924 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...919 days ago
