view oases_optimiser.sh @ 1:070f9de358fc draft

planemo upload for repository https://bitbucket.org/drosofff/gedtools/
author drosofff
date Sun, 21 Jun 2015 15:05:17 -0400
parents eedbe32980bb
children
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#!/bin/bash

min_k=$1
max_k=$2
input=$3
job_dir=$4

for i in `seq $min_k 2 $max_k`
do
     velveth $job_dir/outputFolder_$i $i $input
     velvetg $job_dir/outputFolder_$i -read_trkg yes
     oases $job_dir/outputFolder_$i
done

velveth $job_dir/MergedAssemblyFolder 27 -long outputFolder_*/transcripts.fa
velvetg $job_dir/MergedAssemblyFolder -read_trkg yes -conserveLong yes
oases $job_dir/MergedAssemblyFolder -merge yes