From 24b5752ee57b790ae526e4afa7ec40f4aee54e0b Mon Sep 17 00:00:00 2001
From: Alexis  CRISCUOLO <alexis.criscuolo@pasteur.fr>
Date: Wed, 1 Sep 2021 13:44:18 +0200
Subject: [PATCH] procedure source code for Example

---
 paper/paper.code.txt | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)
 create mode 100644 paper/paper.code.txt

diff --git a/paper/paper.code.txt b/paper/paper.code.txt
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+++ b/paper/paper.code.txt
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+####################################
+## Example: procedure source code ##
+####################################
+
+# downloading PE FASTQ file using wget
+wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR207/009/SRR2079909/SRR2079909_1.fastq.gz
+wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR207/009/SRR2079909/SRR2079909_2.fastq.gz
+
+# trimming/clipping PE FASTQ files using AlienTrimmer (https://research.pasteur.fr/en/software/alientrimmer)
+echo -e ">poly-A\nAAAAAAAAAAAAAAAAAA\n>poly-C\nCCCCCCCCCCCCCCCCCC" > polys.fa
+AlienTrimmer -1 SRR2079909_1.fastq.gz -2 SRR2079909_2.fastq.gz -a polys.fa -q 20 -l 100 -o SRR2079909
+rm SRR2079909.S.fastq polys.fa
+
+# estimating the number FO of distinct k-mers (k=25) using ntCard (https://github.com/bcgsc/ntCard)
+ntcard -t 12 -k 25 -p SRR2079909 SRR2079909.1.fastq SRR2079909.2.fastq
+
+# running ROCK with kappa=45 and kappa' varying from 0 to 8
+rock -k 25      -C 45 -n 105584331 SRR2079909.1.fastq,SRR2079909.2.fastq
+rock -k 25 -c 2 -C 45 -n 105584331 SRR2079909.1.fastq,SRR2079909.2.fastq
+rock -k 25 -c 4 -C 45 -n 105584331 SRR2079909.1.fastq,SRR2079909.2.fastq
+rock -k 25 -c 6 -C 45 -n 105584331 SRR2079909.1.fastq,SRR2079909.2.fastq
+rock -k 25 -c 8 -C 45 -n 105584331 SRR2079909.1.fastq,SRR2079909.2.fastq
+
+# running normalize-by-median (https://github.com/dib-lab/khmer)
+paste  <( paste - - - - < SRR2079909.1.fastq ) <( paste - - - - < SRR2079909.2.fastq ) | tr '\t' '\n' > SRR2079909.i.fastq
+normalize-by-median.py -M 128G -k 25 -C 45 -p -o SRR2079909.khmer.i.fastq SRR2079909.i.fastq 
+
+# running BBnorm (https://sourceforge.net/projects/bbmap)
+bbnorm.sh -Xmx128G in=SRR2079909.1.fastq in2=SRR2079909.2.fastq out=SRR2079909.bbnorm.1.fastq out2=SRR2079909.bbnorm.2.fastq k=25 target=45 threads=12 
+
+# running BigNorm (https://git.informatik.uni-kiel.de/axw/Bignorm)
+Bignorm -1 SRR2079909.1.fastq -2 SRR2079909.2.fastq -b -d 1 -k 25 -C 45 -n 
-- 
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