Results for "BLAST Parser"
Bio-Scripts
(JitMetaENV) ➜ day2 conda install -c bioconda kraken2 Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve...1213 days ago
Set up WGD environment using conda !
#Wgd cannot be installed directly with bioconda at present, so it is slig...depends on the following software #BLAST #MCL #MUSCLE/MAFFT/PRANK #...ster) conda create -n wgd python=3.7 blast mcl muscle mafft prank paml...Commands: dmd All-vs.-all diamond blastp...1200 days ago
Perl script to check perl modules and download NCBI, BUSCO, Taonomy, Silva databases !
...#Install diamondDB __END__ # BlastDB download my $result = `mkd...mp.tar.gz; tar xzfp taxdump.tar.gz`; parseResult ($result); #do your magic here sub parseResult { system ($_[0]); }...d started"; } if [ ! -d "$PWD/blastDB" ]; then if [ ! -d "$PW...1157 days ago
- blastpgp arguments: -d Database [String] default = nr -i...o identities and blunt ends, 7 = XML Blast output, 8 = Tabular output,...fault = stdout -y Dropoff (X) for blast extensions in bits (default i...ault = 250 -C Output File for PSI-BLAST...
947 days ago
Command line to create blast uniref database !
#The NCBI BLAST+ distribution does not include 'blastpgp', it has been replaced by the 'psiblast' program. The 'blastpgp' program is avail...BI's FTP site: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/2.2.26/....0filt -i uniref90filt #When using NCBI BLAST+...947 days ago
Command line to download blast database / protein
#download all available nr - protein database as a single file #Database loc...es are available ftp://ftp.ncbi.nlm.nih.gov/blast/db/ https://ftp.ncbi.nlm.nih.gov/blast/db/ # Database detail / de...o download wget 'ftp://ftp.ncbi.nlm.nih.gov/blast/...940 days ago
Download desire version of Blast software !
#Create a directory and wget it wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-x64-linux.tar.gz #unpacking blast tar -zxvf ncbi-blast-2.6.0+-x64-linux.tar.gz #S...rt OMP_NUM_THREADS=??? module load ncbi-blast/...939 days ago
Downloading mmseqs databases !
# mmseqs databases Usage: mmseqs databases [options] Name Type...Aminoacid - https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA - NT...Nucleotide - https://ftp.ncbi.nlm.nih.gov/blast/...939 days ago
Installing Covid19 Environment !
...##################################################### | 100% perl-xml-parser-2.44 | 165 KB | #########...############################################################## | 100% blast-2.12.0 | 22.4 MB | #...920 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 -db -outfmt '6 std...up the search at the cost of sensitivity: blastn...632 days ago
