Results for "3D Genome"
Bio-Scripts
Tadpole is 250x faster than SPADes assembler !
...It is recommended that mce=1 for low-depth metagenomes. mincountretain=0 (mincr...may yield more accurate genome size estimation. contigpasse...pth data, but they are very slow for large metagenomes. Overlap parameters (for...1003 days ago
- ...Using a YAML File $ conda activate earth-analytics-python $ conda env update -f environment.yml #Adding a Package to your YAML File name: genome-analytics-python channels:...
988 days ago
Installing Covid19 Environment !
...The default QUAST package does not include: * GRIDSS (needed for structural variants detection) * SILVA 16S rRNA database (needed for reference genome detection in metagenomic data...950 days ago
Bash script to simulate a genome !
...embly cd /genetics/elbers/test/fly2 wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/401/745/GCA_0034...CA_003401745.1_ASM340174v1_genomic.fna_upper.diploid.fasta.log.txt # genome size bgzip -@75 -cd GCA_0034...945 days ago
Bash script to split multifasta file !
...ile=sprintf("chunk%d.fa",n);} print >> file; n++; next;} { print >> file; }' < multi.fasta #Another great solution is genome tools (gt), which you can find here: http://genometools.org/, which has the foll...850 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 we s...850 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...662 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-release647 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...544 days ago
Perl script to find inverted repeats !
...ings; use Bio::SeqIO; use Bio::Tools::Run::RepeatMasker; my $genome_file = "genome.fasta"; # read genome sequ...= Bio::Tools::Run::RepeatMasker->new(); my $rm_report = $rm->run($genome_file); # parse RepeatMaske...452 days ago
