Tadpole is 250x faster than SPADes assembler !
...e values are not supported. Specifically, it allows 1-31, mu...may be specified; default is 1. minprob...perform error correction....If it appears that the merge created new...1039 days ago
Run multiple bash command in screen !
#login to screen screen -r 123 #bash.sh srun --partition=compute --nodes=1 --ntasks-per-node=40 --pty bash.sh #Run and check the status in screen contol +A +D1025 days ago
1024 days ago
Trim the reads in loop using Trimmomatic !
...1.fastq.gz do base=$(basename ${infile} _1.fastq.gz) trimmomatic PE ${infile} ${base}_2.fastq.gz...tq.gz \ SLIDINGWINDOW:4:20 MINLEN:25 ILLUMINACLIP:NexteraPE-PE.fa:2:40:15 done1018 days ago
Oneliner to convert lower-case to sequence masked with Ns
perl -pe '/^[^>]/ and $_=~ s/[a-z]/N/g' genomic.fna > genomic.N-masked.fna awk '{if(/^[^>]/)gsub(/[a-z]/,"N");print $0}' genomic.fna > genomic.N-masked.fna1013 days ago
Perl script for Smith-Waterman Algorithm
# Smith-Waterman Algorithm # usage statement die "usage: $0 \n" unless @ARGV == 2; # get sequences from command line my ($seq1, $seq2) = @ARGV; # scoring...1013 days ago
1013 days ago
Command line to create blast uniref database !
...lt -i uniref90filt #When using NCBI BLAST+ the 'formatdb' command should be replaced by the equivalent 'makeblastdb' command: makeblastdb -dbtype prot -in uniref90filt -out un...1013 days ago
Command line to download blast database / protein
....nih.gov/blast/db/ https://ftp.ncbi.nlm.nih.gov/blast/db/ # Database detail / description nr.*tar.gz | Non-redundant protein sequences from GenPept, Swissprot, PIR, PDF, PDB,...1006 days ago
Download desire version of Blast software !
...t tar -zxvf ncbi-blast-2.6.0+-x64-linux.tar.gz #Slurm template #!/bin/bash #SBATCH --partition=longjobs #SBATCH --nodes=1 #SBATCH --ntasks-per-node=32 #SBATCH --time=1:00...1005 days ago