Rmarkdown5

#!/bin bash
# Spring 2019
#Gianna Desrochers

#Choi JY, Groen S, Zaaijer S, Purugganan. Nanopore sequence-based genome assembly o$
#PREJEB28274

#Albacore, NanoPack, Porechop, Canu, bbmap stats.sh, BBTools, BUSCO, FASTQ, bwa-mem$
var='value'
echo $var

datapath=/usr/share/data/proj_data/thale_cress

echo $datapath

ls -lh $datapath

logit=log.txt

echo "Logging to $logit"

touch $logit

echo "Output test" > $logit
cat log.txt

exit

datapath='/usr/share/data/proj_data/example'
outputdir='~/testout'

ls -lh $datapath

#more summary commands and stats:

#Analysis Steps:
#1) raw signal intensity data used for base calling using Albacore
#2)Base-called reads passed the Albacore filter and used by Porechop to cut adapters at the ends of reads
#3)Genome assembly done using Canu 
#4)Genome assembly statistics calculated using bbmap stats.sh from BBTools suite
#5)Genome completeness evaluated via BUSCO
#6)Adapter trimmed FASTQ reads aligned to the unpolished draft genome assembly using bwa-mem 
#7)Nanopolish used for polishing the genome
#8)Program minimap used to align FASTQ reads for draft genome assembly, used by RACON to polish draft genome
#8) ran 8 rounds of RACON and then 7 rounds of Pilon


#Sequencing data: European Nucleotide Archive under bioproject ID PRJEB28274
#How to call centrifuge: centrifuge -i infile.fa -o report.tab