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Program call:
uniref90_subsample.fasta uniref90 mmseqs2_results.m8 tmp -s 4 --max-seqs 4000

MMseqs Version:                    	be8f616d7cfd406880608e470a6c7fda45b04c50
Sub Matrix                         	blosum62.out
Add backtrace                      	false
Alignment mode                     	3
E-value threshold                  	0.001
Seq. Id Threshold                  	0
Coverage threshold                 	0

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files	name
Sample_WB-103.cov.hist.txt	WB_103
Sample_WB-104.cov.hist.txt	WB_104
Sample_WB-105.cov.hist.txt	WB_105
Sample_WB-106.cov.hist.txt	WB_106
Sample_WB-107.cov.hist.txt	WB_107
Sample_WB-108.cov.hist.txt	WB_108
Sample_WB-109.cov.hist.txt	WB_109
Sample_WB-180.cov.hist.txt	WB_180
Sample_WB-181.cov.hist.txt	WB_181

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library(RColorBrewer)
rm(list=ls())
samples = read.table("Samples.txt",header=T,stringsAsFactors=F)
coverage = list()
cumulative_coverage = list()
for (i in 1:length(samples$files)) {
  coverage[[i]] <- read.table(samples$files[i])
  cumulative_coverage[[i]] <- 1-cumsum(coverage[[i]][,5])
}

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#!/usr/bin/env python
# -*- coding: utf-8 -*-

import sys
import os
import cyvcf
import Bio.bgzf


vcf_input = sys.argv[1]

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import net.sf.picard.fastq.FastqReader
import java.io.File
import scala.collection.JavaConversions._

object Reader extends App {
  val file = new File(args(0))
  val fr = new FastqReader(file)
  printToFile(new File(args(1)))(p => {
    for (seq <- fr.iterator()) {
      val header = seq.getReadHeader.split(" ")

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library(biomaRt)

## ensembl=useMart("ensembl")
## listDatasets(ensembl) # show all the possible databases on Ensembl

ensembl = useEnsembl(biomart="ensembl",dataset="btaurus_gene_ensembl")

## listAttributes(ensembl) # show the attributes of the database

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#!/usr/bin/env ruby

require "htsjdk-1.125.jar" # https://github.com/broadinstitute/picard/releases/download/1.125/picard-tools-1.125.zip
require "logger"


java_import "htsjdk.samtools.SAMFileReader"
java_import "htsjdk.samtools.SAMFileWriterFactory"

logger = Logger.new(STDOUT)

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  desc "quant GTF OUTPUTDIR BAM ", "Genes and transcripts quantification"
  Bio::Ngs::Cufflinks::Quantification.new.thor_task(self, :quant) do |wrapper, task, gtf, outputdir, bam|
    wrapper.params = task.options
    wrapper.params = {"num-threads" => 6, "output-dir" => outputdir, "GTF" => gtf }
    wrapper.run :arguments=>[bam], :separator => "="
  end

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      class Trim
        include Bio::Command::Wrapper
        set_program Bio::Ngs::Utils.binary("fastx_trimmer")
        use_aliases
        add_option :first_base, :type => :numeric, :aliases => "-f", :desc => "First base to keep"
        add_option :last_base, :type => :numeric, :aliases => "-l", :desc => "Last base to keep"
        add_option :compress, :type => :boolean, :aliases => "-z", :desc => "Compress output with GZIP"
        add_option :input, :type => :string, :aliases => "-i", :desc => "Input FASTA/Q file", :collapse => true
        add_option :output, :type => :string, :aliases => "-o", :desc => "Output FASTA/Q file", :collapse => true
        add_option :trim, :type => :numeric, :aliases => "-t", :desc => "Trim N nucleotides from the end of the read"

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      def thor_task(klass, task_name, &block)
        if program.nil?
          warn "WARNING: no program is associated with #{class_name.upcase} task, does not make sense to create a thor task."
          return nil
        end          
        if klass
          wrapper = self   
          klass.class_eval do            
            wrapper.options.each_pair do |name, opt|
              method_option name, opt