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...989 days ago
974 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...936 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...931 days ago
838 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...836 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...836 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...836 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 -nr781 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...648 days ago