Results for "Genome Assembly"
Bio-Scripts
Tadpole is 250x faster than SPADes assembler !
...that mce=1 for low-depth metagenomes. mincountretain=0 (mincr)...may yield more accurate genome size estimation. contigpasses=...reads that cannot be used for assembly. This me...y are very slow for large metagenomes. Overlap parameters (for ov...987 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-a...
973 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 d...935 days ago
Bash script to simulate a genome !
...ues/33 # Use Drosophila melongaster PacBio assembly cd /genetics/elbers/test/fly2 wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/401/745/GCA_0034..._genomic.fna_upper.diploid.fasta.log.txt # genome size bgzip -@75 -cd GCA_003401...929 days ago
- (abhiENV) [abhi@hn1 output_OM824]$ conda create -n mgsc python=3.6 graphviz numpy Co...active environment, use # # $ conda deactivate mgsc -i [path to your assembly graph] -o [output directory n...
836 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://genometo...835 days ago
Install StringTie on ubuntu / Linux !
#StringTie is a software program to perform transcript assembly and quantification of RNAseq data. The binary distributions are available so to install we can just download this distribution and e...835 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 I...835 days ago
Bash command to explore assembly summary genbank !
wget https://ftp.ncbi.nlm.nih.gov/genomes/genbank/assembly_summary_genbank.txt pip3 install csvkit csvcut -t -K 1 -c 'excluded_from_refseq' assembly_summary_genbank.txt \ | tail -n +2 | tr ";" "\n" \ | sed -e 's/^ //' -e 's/ $//' | grep -v '""' \ | sort | uniq -c | sort -nr780 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...647 days ago
