Results for "Assembly"

Bio-Scripts

  • Download the genome from NCBI using bash script/command

    ...cd genome # Look for genome assembly summary and extract the URL...nlm.nih.gov/genomes/refseq/fungi/assembly_summary.txt' | awk '{FS="\t"}...nih.gov/genomes/genbank/bacteria/assembly_summary.txt' | awk '{FS="\t"}....nih.gov/genomes/refseq/protozoa/assembly_summary.txt' | awk '{FS="\t"}...

    2495 days ago

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

    ...genome_gff # Look for genome assembly summary and extract the URL...nlm.nih.gov/genomes/refseq/fungi/assembly_summary.txt' | awk '{FS="\t"}...nih.gov/genomes/genbank/bacteria/assembly_summary.txt' | awk '{FS="\t"}....nih.gov/genomes/refseq/protozoa/assembly_summary.txt' | awk '{FS="\t"}...

    2486 days ago

  • Create genome scaffolding with Perl

    ...rbose => 0}); } } @ARGV = @pslFiles; if(!$projOpts->{"query"}){ pod2usage({-exitVal => 1, -message => "Error: No query assembly file provided",...

    2271 days ago

  • Running Transrate !

    ...alyse a de-novo transcriptome assembly using three kinds of metrics: 1. sequence based (if --assembly is given) 2. read mapping ba...explanations ➜ BorisTrinityAssembly /home/urbe/Tools/transrate-1....a/urbe/MyPassport/BorisTrinityAssembly/transrateSTAT/Trinity/contigs...

    2086 days ago

  • Resume the MIRA assembler run !

    ......] Options: -c / --cwd= directory Change working directory -r / --resume Resume an interupted assembly -h / --help...

    1697 days ago

  • Running REAPR !

    .../urbe/Tools/Reapr_1.0.18/reapr score -P 5 00.assembly.fa.gaps.gz 00.in.bam 01.stats.../home/urbe/Tools/Reapr_1.0.18/reapr break 00.assembly.fa 03.score.errors.gff.gz 04..../urbe/Tools/Reapr_1.0.18/reapr score -P 5 00.assembly.fa.gaps.gz 00.in.bam 01.stats...

    2062 days ago

  • Downloading GATK !

    ...Call germline SNPs and indels via local re-assembly of haplotypes HaplotypeC...Call somatic SNVs and indels via local assembly of haplotypes ReadsPipel...

    2038 days ago

  • Installing pb-assembly on Linux !

    ...rayan@hmem00 ~]$ conda install -c bioconda pb-assembly Fetching package metadata .....issing in current linux-64 channels: - pb-assembly -> genomicconsensus -> python...p h470a237_0 conda-forge pb-assembly 0.0.1...

    1997 days ago

  • Test bp-assembly !

    (denovo_asm) [jnarayan@hmem00 ~]$ git clone https://github.com/cdunn2001/git-sym.git fatal: destination path 'git-sym' already exists and is not an empty directory. (d...

    1997 days ago

  • Setting up falconUnzip conda environments for genome assembly !

    ...d / updated specs: - pb-assembly The following packages w...18 KB conda-forge pb-assembly-0.0.2 | py...conda-forge pb-assembly: 0.0.2-py27_0...################# | 100% pb-assembly-0.0.2 | 4 KB | ######...

    1953 days ago