diff --git a/READ_THIS b/READ_THIS
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index 0000000000000000000000000000000000000000..5f3a34a5941e231403eb410cd6012a9fb90af9db
--- /dev/null
+++ b/READ_THIS
@@ -0,0 +1 @@
+There are a number of useful scripts on /projet/genosol/work/script on the migale server. I chmod 777 the access to all of my files . 
diff --git a/bwa b/bwa
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index 0000000000000000000000000000000000000000..110d827188a17cf4551d52ce84cb5af4ffe506f1
--- /dev/null
+++ b/bwa
@@ -0,0 +1,11 @@
+conda activate bwa-0.7.17
+
+bwa index -a bwtsw solca_95p200bp.fasta
+bwa aln -t 8 [SCAFFOLD.fasta] R1.gz | awk '{if($3!="*"){print $0}}' > OUT1.sai
+bwa aln -t 8 [SCAFFOLD.fasta] R2.gz| awk '{if($3!="*"){print $0}}' > OUT2.sai
+bwa sampe [SCAFFOLD.fasta] OUT1.sai OUT2.sai R1.gz R2.gz > OUT.sam
+samtools view -F 4 -Sb  OUT.sam  | samtools sort > OUT.bam
+samtools depth OUT.bam  > temp.depthmore
+samtools idxstats OUT.bam  > reads_per_scaffold.txt
+
+conda deactivate
diff --git a/kaiju b/kaiju
new file mode 100644
index 0000000000000000000000000000000000000000..9a7095da2007b3e5e4bf674f2612811605181ff2
--- /dev/null
+++ b/kaiju
@@ -0,0 +1,12 @@
+conda activate kaiju-1.7.3
+##for multiple files
+conda activate kaiju-1.7.2
+for i in {1..10}
+do
+kaiju -i *"$i"*R1*.fastq.gz -j *"$i"*R2*.fastq.gz -t /db/outils/kaiju-1.7.0/nr/nodes.dmp -f /db/outils/kaiju-1.7.0/nr/kaiju_db_nr.fmi  -z 6 -o fraggenescan_"$i"_kaijuNR
+
+#add Taxon names
+addTaxonNames -t /db/outils/kaiju-1.7.0/nr/nodes.dmp -n /db/outils/kaiju-1.7.0/nr/names.dmp -i fraggenescan_"$i"_kaijuNR -r superkingdom,genus,species -o kaiju_"$i"_names.out
+kaijuReport -t /db/outils/kaiju-1.7.0/nr/nodes.dmp -n /db/outils/kaiju-1.7.0/nr/names.dmp -i fraggenescan_"$i"_kaijuNR -l superkingdom,phylum,class,family,genus -r genus -o kaiju.out.summary_"$i"_3.txt
+kaijuReport -t /db/outils/kaiju-1.7.0/nr/nodes.dmp -n /db/outils/kaiju-1.7.0/nr/names.dmp -i fraggenescan.kaijuNR -p -r genus -o kaiju.out.summary_"$i"_4.txt
+done
diff --git a/mapping.sh b/mapping.sh
new file mode 100644
index 0000000000000000000000000000000000000000..65272e73664d0806fb507a39de034f71b5d5affe
--- /dev/null
+++ b/mapping.sh
@@ -0,0 +1,18 @@
+
+
+mkdir mapXXb1meg
+cd mapXXb1meg/
+cp ../solcab1_95id200bp.fasta solcab1_95id200bp.fasta
+bwa index -a bwtsw solcab1_95id200bp.fasta
+bwa aln -t 8 solcab1_95id200bp.fasta ../*XX*R1*.fastq.gz | awk '{if($3!="*"){print $0}}' > OUT1.sai
+bwa aln -t 8 solcab1_95id200bp.fasta ../*XX*R2*.fastq.gz | awk '{if($3!="*"){print $0}}' > OUT2.sai
+bwa sampe solcab1_95id200bp.fasta OUT1.sai OUT2.sai ../*XX*R1*.fastq.gz ../*XX*R2*.fastq.gz > OUT.sam
+samtools view -F 4 -Sb  OUT.sam  | samtools sort > OUT.bam
+samtools depth OUT.bam  > temp.depthmore
+samtools idxstats OUT.bam  > reads_per_scaffoldXXb1meg.txt
+#Use for Tablet view
+samtools view -F 4 -bS OUT.sam -t solcab1_95id200bp.fasta | samtools sort > OUT_tablet.bam
+samtools sort OUT_tablet.bam -o sorted.bam
+samtools index sorted.bam
+
+rm -fr OUT1.sai OUT2.sai OUT.sam OUT.bam temp.depthmore
diff --git a/megahit_metaG b/megahit_metaG
new file mode 100644
index 0000000000000000000000000000000000000000..be341e74cbbcf83f4f81023dcf4d97c2d7f8b045
--- /dev/null
+++ b/megahit_metaG
@@ -0,0 +1,4 @@
+conda activate megahit-1.2.9
+##Yes, its that simple
+megahit -1 R1.fastq.gz -2 R2.fastq.gz -o [OUTPUT]
+conda deactivate 
diff --git a/mget_mput b/mget_mput
new file mode 100644
index 0000000000000000000000000000000000000000..5a508df5dc82aadb3791e36b1cf338a8238157b1
--- /dev/null
+++ b/mget_mput
@@ -0,0 +1,15 @@
+sftp username@server << EOT
+#example
+cd /backup/SOLCA/mRNA
+mput RNA*-mRNA*
+bye
+EOT
+
+
+
+sftp username@server << EOT
+#example 
+cd /backup/SOLCA/mRNA
+mget *67*split*
+bye
+EOT
diff --git a/simka b/simka
new file mode 100644
index 0000000000000000000000000000000000000000..a63dc576f4247923f6c8b6a5c854be3b125e75eb
--- /dev/null
+++ b/simka
@@ -0,0 +1,20 @@
+# creates liste of the samples. 
+ls *subset* > temp
+#creates right format for SIMKA
+awk -v var=$(pwd) '{print "id"NR": "var"/"$0}' temp > liste
+conda activate simka-1.5.2
+### Kmersize can be optimized for the sample, default is 21, tmp files can be kept, but is not necessary. 
+[location]/bin/simka -in [liste] -out simka_out -out-tmp simka_temp -keep-tmp -kmer-size 30 -nb-cores 4 -max-reads [number]
+
+### R script to make figure
+### REMOVE FIRST ; IN CSV FILES!!!!
+a<-as.matrix(read.table("file.csv",sep=";",header=T))
+#list
+rownames(a)<- c("samplename1","samplename2")
+colnames(a)<- c("samplename1","samplename2")
+#plot
+heatmap(a,trace="none", Rowv=F)
+#print plot
+pdf("name.pdf", width=15, height=15)
+heatmap(a,trace="none", Rowv=F)
+dev.off()
diff --git a/sortmerna b/sortmerna
new file mode 100644
index 0000000000000000000000000000000000000000..0dada9b113ecf814c037f70f2d7a12e98d91ec9f
--- /dev/null
+++ b/sortmerna
@@ -0,0 +1,9 @@
+###in case of conda enviroment. Check version when first using the software (conda info --envs | grep [NAME SOFTWARE])
+conda activate sortmerna-4.2.0
+
+###Check location databes if migale is not used
+sortmerna -threads 8 -v --reads [FASTQ OR .GZ] --paired_in --aligned FILE_NAME.extendedFrags-rRNA --other FILE_NAME.extendedFrags-mRNA --fastx --ref/usr/local/genome/src/sortmerna-2.0/rRNA_databases/rfam-5s-database-id98.fasta,/projet/mig/work/orue/SORTMERNA_index/index/rfam-5s:/usr/local/genome/src/sortmerna-2.0/rRNA_databases/rfam-5.8s-database-id98.fasta,/projet/mig/work/orue/SORTMERNA_index/index/rfam-5.8s:/usr/local/genome/src/sortmerna-2.0/rRNA_databases/silva-arc-16s-id95.fasta,/projet/mig/work/orue/SORTMERNA_index/index/silva-arc-16s-id95:/usr/local/genome/src/sortmerna-2.0/rRNA_databases/silva-arc-23s-id98.fasta,/projet/mig/work/orue/SORTMERNA_index/index/silva-arc-23s-id98:/usr/local/genome/src/sortmerna-2.0/rRNA_databases/silva-bac-16s-id90.fasta,/projet/mig/work/orue/SORTMERNA_index/index/silva-bac-16s-id90:/usr/local/genome/src/sortmerna-2.0/rRNA_databases/silva-bac-23s-id98.fasta,/projet/mig/work/orue/SORTMERNA_index/index/silva-bac-23s-id98:/usr/local/genome/src/sortmerna-2.0/rRNA_databases/silva-euk-18s-id95.fasta,/projet/mig/work/orue/SORTMERNA_index/index/silva-euk-18s-id95:/usr/local/genome/src/sortmerna-2.0/rRNA_databases/silva-euk-28s-id98.fasta,/projet/mig/work/orue/SORTMERNA_index/index/silva-euk-28s-id98
+
+conda deactivate
+
+