Results for "Comparative Genomes"

Bio-Scripts

  • Download the genome from NCBI using bash script/command

    ...l 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/fungi/assembly_summary...s|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_geno...l 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/plant/assembly_summary...s|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_geno...

    2494 days ago

  • Download the gff files from NCBI using bash script/command

    ...l 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/fungi/assembly_summary...s|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_geno...l 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/plant/assembly_summary...s|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_geno...

    2485 days ago

  • Loop over with all files in a directory in bash

    #!/bin/bash FILES=/media/ComparativeGenomics/ncbi-genomes-2017-11-13/* ref=/media/ComparativeGenomics/ncbi-genomes-2017-11-13/GCA_000196735.1_ASM19673v1_genomic.fna path=/home/urbe/Tools/SATSUMA/satsuma-code-0 for f in...

    2293 days ago

  • Download genomes in batch from NCBI

    curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/bacteria/assembly_summary.txt' | awk '{FS="\t"} !/^#/ {print $20}' | sed -r 's|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/)(GCA/)([0-9]{3}/)([0-9]{3}/)([0-9]{3}/)(GCA_.+)|\1\2\3\4\5\6/\6_genomic.fna.gz|' > genomic_file

    2225 days ago

  • Fastq-dump for SRA download

    ➜ bin git:(master) ✗ ./fastq-dump --help Usage: ./fast...-filter Filter used in early 1000 Genomes data: no...er-1 Filter used in current 1000 Genomes data Filters based on ali...

    2088 days ago

  • Running Transrate !

    ➜ BorisTrinityAssembly /home/urbe/Tools/transrate-1.0.3-linux-x86_64/transrate _...ad diagnostics [ INFO] 2018-07-13 14:54:34 : No reference provided, skipping compara...

    2085 days ago

  • Downloading GATK !

    jitendra@jitendra-UNLOCK-INSTALL[SNP] wget https://github.com/broadinstitute/gatk/releases/download/4.0.2.1/gatk-4.0.2....ty Control: Tools that collect sequencing quality related and compara...

    2037 days ago

  • Pack a perl program with their dependencies on Ubuntu !

    ...assemblies of hundreds of microbial genomes and highly contiguous reconstruct...of many dozens of plant and animal genomes, enabling new insights into evolu...ere: https://www.lazoi.com/Home Comparative Genomics !!This group is dedicated to Comparative genomics ... Dramatic res...

    1473 days ago

  • Bash script to simulate a genome !

    # Reference https://github.com/chhylp123/hifiasm/issues/33 # Use Drosophila melongaste...io assembly cd /genetics/elbers/test/fly2 wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/401/745/GCA_00340...

    880 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 -nr

    730 days ago