Print the screenshot of read coverage remotely !
#Chrom_2:9700000-9760000 ASCIIGenome -ni --fasta A_vaga.NDPD.fasta -r Chrom_2:9700000-9760000 -x "save >> test.pdf" A_vaga.NDPD.fasta.out.sam.bam.sorted.bam1293 days ago
1213 days ago
Perl script to check perl modules and download NCBI, BUSCO, Taonomy, Silva databases !
...min/silva_databases/release_138_1/Exports/SILVA_138.1_LSUParc_tax_silva.fasta.gz'; my $silva_LSU_fileName = 'SILVA_138.1_LSUParc_tax_silva.fasta.gz'; my $silva_LSU_code =...1170 days ago
Corona variant calling steps !
...ed_fastq_small/" find "$FILE_PATH" -name "*.fasta" | while IFS= read -r my_fi..."$my_file") basename=$(basename "$my_file" .fasta) echo $basename mkdir...bcf/$basename.bcf -f data/ref_genome/sequences.fasta results/bam/$basename.sorted....1054 days ago
Perl onliner to print fasta headers !
#Save all your fasta in seq.fa and run the following ... perl -ne 'print if /^>/' seq.fa #Print header with line number perl -ne 'print "$. $_" if /^>/ ' seq.fa1006 days ago
Python script to read FASTA and FASTQ file !
...*- coding: utf-8 -*- from pysam import FastxFile def read_fasta_q_file(fasta_q_file): """Parse FASTA/...am.FastxFile`. Args: fasta_q_file (str): Path to FASTA/Q file. """ with...986 days ago
Tadpole is 250x faster than SPADes assembler !
...gs. dot= Write a contigs connectivity graph (partially implemented) dump= Write kmers and their counts. fastadump=t Write kmers and counts as fasta versus 2-column tsv. mincoun...986 days ago
960 days ago
Command line to create blast uniref database !
...ftp.ncbi.nlm.nih.gov/blast/executables/release/2.2.26/. wget ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz gunzip -v uniref90.fasta.gz bin/pfilt uniref90.fasta...960 days ago
Downloading mmseqs databases !
...Aminoacid - https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA - NT Nucleotide - https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA - PDB Amino...952 days ago