Results for "New Genome"
Bio-Scripts
Tadpole is 250x faster than SPADes assembler !
...that mce=1 for low-depth metagenomes. mincountretain=0 (mi...may yield more accurate genome size estimation. contigpasse...y are very slow for large metagenomes. Overlap parameters (for...ppears that the merge created new errors, undo it. Java Paramet...978 days ago
- #Create a conda environment. #Install a Python package in the terminal using conda...a env update -f environment.yml #Adding a Package to your YAML File name: genome-analytics-python channels:...
963 days ago
Installing Covid19 Environment !
(base) vikas@vikas-Lenovo-ideapad-320-15ISK:~/vinodLab/Genepi$ conda env create -f...structural variants detection) * SILVA 16S rRNA database (needed for reference genome detection in metagenomic data...925 days ago
Bash script to simulate a genome !
# Reference https://github.com/chhylp123/hifiasm/issues...elbers/test/fly2 wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/401/745/GCA_0034...0174v1_genomic.fna_upper.diploid.fasta.log.txt # genome size bgzip -@75 -cd GCA_0034...920 days ago
Bash script to split multifasta file !
#Using awk, we can easily split a file (multi.fa) into chunks of size...;} { print >> file; }' < multi.fasta #Another great solution is genome tools (gt), which you can find here: http://genometools.org/, which has the foll...825 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 Unive...825 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...637 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-release622 days ago
Identify genome-wide synteny with LASTZ alignment
#This is the walkstrough how to identifiy genome-wide synteny markers based on LASTZ alignment. Step1：Mask the repeat sequences for both genomes and chromosomes. RepeatMa...519 days ago
Perl script to find inverted repeats !
...Bio::Tools::Run::RepeatMasker; my $genome_file = "genome.fasta"; # read genome sequence my $seqio = Bio::SeqIO->new(-file => $genome_file, -format =...y $rm = Bio::Tools::Run::RepeatMasker->new(); my $rm_report = $rm->run($genome_file); # parse RepeatMaske...427 days ago
