Results for "Filter"

Bio-Scripts

  • Perl script to calculate N50

    ...use strict; use Getopt::Long; use Bio::SeqIO; my $fasta_file; my $filter_length; GetOptions("fasta_file=s" => \$fasta_file, "length_filter=i" => \$filter_length); die...

    2667 days ago

  • Perl script to run SATSUMA in loop !

    #!/usr/bin/perl -w use strict; use File::Temp qw(tempfile); # Usage perl 1by1.pl for SATSUMA analysis # User need to set the reference multifasta file name here...

    2103 days ago

  • Fastq-dump for SRA download

    ...to individual reads Full Spot Filters Applied to...t id --spot-groups Filter by SPOT_GROUP (member): name[...or ending with >= 10N --qual-filter-1 Filter use...GROUP (member name) -R|--read-filter Split into files by REA...

    2089 days ago

  • Perl script to merge LastZ overlaps

    #!/usr/bin/perl use strict; use warnings; use 5.010; # Filter out the exact/direct overlaps from tab seperated alignment file. (lastz format=general- ready) # Do not inclide header in lastz outfile # USAGE: perl filterOverlaps.pl infile > outfile open my $fh, '

    2088 days ago

  • Downloading GATK !

    ...Generates table of filtered base counts at het sites fo...pass quality thresholds and Illumina-specific filters. CollectQualityYieldM...ASTQ file to an unaligned BAM or SAM file FilterSamReads (Picard)...

    2038 days ago

  • Install vcftools on Ubuntu

    ...8.3-2ubuntu0.1) ... #MORE at https://vcftools.github.io/perl_module.html # Calculate stats separately for the filter field, quality and non-indels vcf-stats file.vcf.gz -f FILTER,QUAL=10:200,INFO/INDEL=False...

    1488 days ago

  • Setting up autoConTAMPR !

    (base) jit@jit-HP-Pro-3335-MT:~/Downloads/testDock$ docker build -t autocontampr . Sending build context to Docker daemon 9.024MB Step 1/16 : FROM ubuntu:14.04 ---...

    1404 days ago

  • Install prokka using conda !

    (JitMetaENV) ➜ assembly conda install -c bioconda prokka Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen so...

    1178 days ago

  • Tadpole is 250x faster than SPADes assembler !

    ...ounttodump=1 Only dump kmers with at least this depth. showstats=t Print assembly statistics after writing contigs. Prefiltering parameters: prefilter=0 If set to a positiv...

    938 days ago

  • blastpgp arguments !

    ...1 for single hit 1-pass, 2 for 2-pass [Integer] default = 0 -F Filter query sequence with SEG [Stri...ch of database to list of GI's [String] Optional -U Use lower case filtering of FASTA sequence [T/F] O...

    913 days ago