Install grabseqs using conda !
vik@vik-Lenovo-ideapad-320-15ISK:~/Downloads/setu/setu$ conda install grabseqs -c louiejtaylor -c bioconda -c conda-forge Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists.1068 days ago
995 days ago
Remove dupcates in multifasta file !
#Using seqkit for duplicate sequence removal seqkit rmdup -n seqs.fa -o seqs_without_duplicate.fa #Awk for duplicate sequence removal awk '/^>/ { f = !a[$0]++ } f' seqs.fa990 days ago
Tadpole is 250x faster than SPADes assembler !
...Write a contigs connectivity graph (partially implemented) dump= Write kmers and their counts. fastadump=t Write kmers and c...unt below this will have its quality reduced. markdeltaonly=t (mdo...990 days ago
964 days ago
Get the Linux system information !
...;; 3 ) if [[ $(id -u) -eq 0 ]]; then result=$(du -sh /home/* 2> /dev/null)...result "Home Space Utilization (All Users)" else result=$(du -sh $HOME 2> /dev/null)...962 days ago
Command line to download blast database / protein
...are available ftp://ftp.ncbi.nlm.nih.gov/blast/db/ https://ftp.ncbi.nlm.nih.gov/blast/db/ # Database detail / description nr.*tar.gz | Non-redundant protein sequences from G...957 days ago
Download desire version of Blast software !
...#SBATCH --job-name=vsearch #SBATCH -o result_%N_%j.out #SBATCH -e result_%N_%j.err export SBATCH_EXPORT=NONE export OMP_NUM_THREADS=??? module load ncbi-blast/2.6.0_x86_6...956 days ago
Downloading mmseqs databases !
...ew-pfam-b-is-released - eggNOG Profile - http://eggnog5.embl.de - dbCAN2 Profile - http://bcb.unl.edu/dbCAN2 - Resfinder...956 days ago
942 days ago