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05-Genome_cleaning.md

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Genome cleaning

During genome assembly, we encountered some poorly assembled regions due to the genomic structure (repeats) of the OsHV-1 virus. We observed additional sequences upstream (5') of UL. Parts of the genome showed N (named polyN). As well as the junction of UL (named polyC). To understand the origin of this scaffolding and to solve them we proceeded as follows.

Correction of sequences upstream (5') from UL

There are 56 bp upstream corresponding to the extension of the read overlap with UL. These outgoing sequences correspond to the fact that the UL is surrounded by 2 sequences in reverse complement of each other. The assembler will thus extend these sequences during the compaction of the de burjin graph.

Upstream_corrected

Once the UL contiguous orientation is correct the sequences have been corrected using the sed function as follows.

sed -i "s/CTGAGTATCAATTCGAAGTAATCTCCTATACCCAAATCATTACACATCTCGTGCA//" # removed what is out of place in 5'

Resolution of the polyN part

In the structure of the OsHV-1 genome there are small tandem repeated sequences of about 160 bp in the TRs (A, B) and IRs (C) regions. These regions lead to the introduction of 'N' in the sequence assembly in some samples (D).

polyN_presentation

Verification of the assembly by aligning the reads on the de novo assembly genome

First we looked at the alignment of the reads against the assembled scaffold and we were interested in the polyN part.

while read h f; do r1=`ls /PATH/OshV-1-molepidemio/raw/${h}*_R1.fastq.gz`; r2=`ls /PATH/OshV-1-molepidemio/raw/${h}*_R2.fastq.gz`; qsub -v "id=${f}, reads1=${r1}, reads2=${r2}, outdir=, Genome=, outputName=${f}" mappingfastq_bowtie.pbs ; done < OshV-1-molepidemio/raw/b-raw_metadatas/ID_experiment.csv

Where mappingfastq_bowtie.pbs correspond to classique analyse of aligning reads against a genome (OsHV-1 µVar A) as follow:

if [ ! -f ${Genome}.1.bt2 ]
then
    echo -e '\n Building genome index... \n'
    bowtie2-build $Genome $Genome
fi

echo -e "Aligning $(basename $reads1) & $(basename $reads1) against $(basename $Genome)" >> $logfile
bowtie2 -p $NCPUS -x $Genome \
-1 ${reads1} \
-2 ${reads2} | \
samtools view -F 4 -@ $NCPUS -b > ${outputName}.bam \
    2>> ${logfile}
echo -e "Aligning $(basename $reads1) & $(basename $reads1) against $(basename $Genome)" >> $logfile
samtools sort -T ${outputName}.bam -o ${outputName}_sort.bam ${outputName}.bam
samtools flagstat ${outputName}_sort.bam >> ${logfile}

# Visualization in local using ugene
ugene -ui ${bamfile}_sort.bam

We observed (see below) that there were no reads that could cross this ployN.

polyN_presentation

Verification of the assembly by aligning the reads on the previously assembled genome

Then we looked at how to align the reads in this region (560bp) of the OsHV-1 µVar A genome.

while read h f; do r1=`ls /PATH/OshV-1-molepidemio/raw/${h}*_R1.fastq.gz`; r2=`ls /PATH/OshV-1-molepidemio/raw/${h}*_R2.fastq.gz`; qsub -v "id=${f}, reads1=${r1}, reads2=${r2}, outdir=, Genome=/PATH/OshV-1-molepidemio/raw/a-OsHV-1-NCBI-genome/Ostreid_herpesvirus_1_strain_microVar_variant_A_complete_genome_0.fa, outputName=${f}" mappingfastq_bowtie.pbs ; done < OshV-1-molepidemio/raw/b-raw_metadatas/ID_experiment.csv

The reads are correctly aligned in this region (see below) demonstrating both that the assembled consensus genome is similar to the previously assembled genome in this section and that the assembler failed to resolve this region.

polyN_presentation_oshv_uVar

For the samples Thau_2018_NSI_milling_ind1_noPCR and Thau_2018_NSI_milling_ind3_noPCR, which have deletions in the consensus on the polyN region present the different configurations, it will have been arbitrarily chosen to take the sequence corresponding to the OsHV-1µVar A.

Resolution of the polyC part

In some genomes we have been able to observe the presence of incoherence which seems to be due to the presence of a variable length C trac (called polyC).

polyC_presentation

We suspect that the C number in this region is highly variable in the OsHV-1 genome. We therefore made the choice to base the sequence selection on the observation of whole reads overlapping the 'C'.

Example of Thau_2018_NSI_broyage_ind1_noPCR

polyC_presentation

Example of Thau_2018_NSI_broyage_ind3_noPCR

polyC_presentation

Modification of the sequences of the different genomes

For the individual 1 Thau 2018 the sequences that will be modified are

Region PolyN

Thau_2018_NSI_broyage_ind1_quasi-assembly_pilon_pilon cggaaatgattgctgattggttga-------------------------------------------------------------------------------------------------------------------atgtgatatcatctacctccgcaat

NR-genome_Ostreid_herpesvirus_1_strain_microVar_variant_A cggaaatgattgctgattggttgaatgtgatatcatctacctccgcaatgtgttgattgggttgttattattagaccattacttcactctaaaaatataaaccaatgactgtagtcggaaatgattgctgattggttgaatgtgatatcatctacctccgcaat

Region Ul-polyC

This region appears to be complex ACTACAGATATATCTCTAGTGTCAGCCTCTTCAATTACATTGGCAAATGTGCAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGATCTACCATCAATTCCTTGGCCAAAAAATGGTTTAAACCAAACACACA

I'm going to cut between the AAACACA and the AAA

Overlaping reads used to confirmed sequence

> A00977:28:H2VGTDSXY:4:2661:13774:35806
CCTTGGCCAAAAAATGGTTTAAACCAAACACACACCCCCCCCCCCCCCAAACAAAGGGAAGATAAC

From 4447 to 4508
Length: 62
Row: 1
Cigar: 34M4I28M
Strand: complement

-> AAACACACACACACACCCCCCCCCCCCCCCCCCCCCCCCAAA if the interest portion is restricted to the interest portion.

Sequence change code

export PATH=/appli/anaconda/3.7/bin/:$PATH
source activate seqkit
cd PATH/2020-04-29_final_genome
# Thau ind 1
genome=PATH/2020-04-28-asm_polish_2/Thau_2018_NSI_broyage_ind1_noPCR_asm_polished_contigs.fasta
echo -e ">Thau_2018_NSI_broyage_ind1_noPCR_NR-genome" > Thau_2018_NSI_broyage_ind1_noPCR_NR-genome.fasta
# permet de linéariser la séquence
seqkit seq --seq $genome | sed ':a;N;$!ba;s/\n//g' >> Thau_2018_NSI_broyage_ind1_noPCR_NR-genome.fasta
sed -i 's/ACTACAGATATATCTCTAGTGTCAGCCTCTTCAATTACATTGGCAAATGTGCAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGATCTACCATCAATTCCTTGGCCAAAAAATGGTTTAAACCAAACACACA//' Thau_2018_NSI_broyage_ind1_noPCR_NR-genome.fasta
sed -i 's/CGGAAATGATTGCTGATTGGTTGAATGTGATATCATCTACCTCCGCAAT/CGGAAATGATTGCTGATTGGTTGAATGTGATATCATCTACCTCCGCAATGTGTTGATTGGGTTGTTATTATTAGACCATTACTTCACTCTAAAAATATAAACCAATGACTGTAGTCGGAAATGATTGCTGATTGGTTGAATGTGATATCATCTACCTCCGCAAT/' Thau_2018_NSI_broyage_ind1_noPCR_NR-genome.fasta

For the individual 3 Thau 2018 the sequences that will be modified

Region PolyN

NR-genome_Ostreid_herpesvirus_1_strain_microVar_variant_B tcggaaatgattgctgattggttgaatgtgatatcatctacctccgcaatgtgttgattgggttgttattattagaccattacttcactctaaaaatataaacca

Thau_2018_NSI_broyage_ind3_quasi-assembly_pilon_pilon tcggaaatgattgctgattggttgaatg----------------------nnnnnnnttgggttgttattattagaccattacttcactctaaaaatataaacca

Region Ul-polyC

This region appears to be complex ACACACCCCCCCCCCTCTTCCCCAATAAAAGCTTTATGGTGCCGCCTAAAACCTGAGTTTGCTAGTTTTGGACTTTTTTGATATACTATAGTAATCTNNNNNNNNNNNNNNNNNNNNNNNNNNNN

I'm going to cut between the AAACACACA and the AAA

Overlaping reads used to confirmed sequence

> A00977:28:H2VGTDSXY:4:2565:19605:19351
TCCTTGGCCAAAACATGGTTTAAACCAAACACACCCCCCCCCCCCCCCCCCCCCCAAACAAAGGGAAGATAACTCATGTGTTTTATA

From 4446 to 4522
Length: 77
Row: 10
Cigar: 35M10I42M
Strand: complement

-> AAACCAAACACACCCCCCCCCCCCCCCCCCCCCCAAA if the interest portion is restricted to the interest portion.

Sequence change code

export PATH=/appli/anaconda/3.7/bin/:$PATH
source activate seqkit
cd PATH/2020-04-29_final_genome
# Thau ind 3
genome=PATH/2020-04-28-asm_polish_2/Thau_2018_NSI_broyage_ind3_noPCR_asm_polished_contigs.fasta
echo -e ">Thau_2018_NSI_broyage_ind3_noPCR_NR-genome" > Thau_2018_NSI_broyage_ind3_noPCR_NR-genome.fasta
# permet de linéariser la séquence
seqkit seq --seq $genome | sed ':a;N;$!ba;s/\n//g' >> Thau_2018_NSI_broyage_ind3_noPCR_NR-genome.fasta
sed -i 's/ACACACCCCCCCCCCTCTTCCCCAATAAAAGCTTTATGGTGCCGCCTAAAACCTGAGTTTGCTAGTTTTGGACTTTTTTGATATACTATAGTAATCTNNNNNNNNNNNNNNNNNNNNNNNNNNNN//' Thau_2018_NSI_broyage_ind3_noPCR_NR-genome.fasta
sed -i 's/TCGGAAATGATTGCTGATTGGTTGAATGNNNNNNNTTGGGTTGTTATTATTAGACCATTACTTCACTCTAAAAATATAAACCA/TCGGAAATGATTGCTGATTGGTTGAATGTGATATCATCTACCTCCGCAATGTGTTGATTGGGTTGTTATTATTAGACCATTACTTCACTCTAAAAATATAAACCA/' Thau_2018_NSI_broyage_ind3_noPCR_NR-genome.fasta

For the individual 5 Thau 2018 the sequences that will be modified

Region PolyN

NR-genome_Ostreid_herpesvirus_1_strain_microVar_variant_B tgctgattggtctgttattattagaccattacatttattctaaaaatataaaccaatgactgtagtcggaaatgattgctgattggttgaatgtgatatcatctacctccgcaatgtgttgattgggttgttattattagaccattacttcactctaaaaatataaaccaatgactgtagtcggaaatg

Thau_2018_NSI_broyage_ind5_quasi-assembly_pilon_pilon tgctgattggtctgttattattagaccattacatttattctaaaaatataa-------------------------------------------------------------------------------------------------------------------accaatgactgtagtcggaaatg

Sequence change code

export PATH=/appli/anaconda/3.7/bin/:$PATH
source activate seqkit
cd PATH/2020-04-29_final_genome
# Thau ind 5
genome=PATH/2020-04-28-asm_polish_2/Thau_2018_NSI_broyage_ind5_noPCR_asm_polished_contigs.fasta
echo -e ">Thau_2018_NSI_broyage_ind5_noPCR_NR-genome" > Thau_2018_NSI_broyage_ind5_noPCR_NR-genome.fasta
# permet de linéariser la séquence
seqkit seq --seq $genome | sed ':a;N;$!ba;s/\n//g' >> Thau_2018_NSI_broyage_ind5_noPCR_NR-genome.fasta
sed -i 's/TGCTGATTGGTCTGTTATTATTAGACCATTACATTTATTCTAAAAATATAAACCAATGACTGTAGTCGGAAATG/TGCTGATTGGTCTGTTATTATTAGACCATTACATTTATTCTAAAAATATAAACCAATGACTGTAGTCGGAAATGATTGCTGATTGGTTGAATGTGATATCATCTACCTCCGCAATGTGTTGATTGGGTTGTTATTATTAGACCATTACTTCACTCTAAAAATATAAACCAATGACTGTAGTCGGAAATG/' Thau_2018_NSI_broyage_ind5_noPCR_NR-genome.fasta

For the individual 6 Thau 2018 the sequences that will be modified

Region PolyN

NR-genome_Ostreid_herpesvirus_1_strain_microVar_variant_B gaaatgattgctgattggttgaatgtgatatcatctacctccgcaatgtgttgattgggttgttattattagaccattacttcactctaaaaatataaaccaatgactgtagtcggaaatgattgctgattggttgaatgtgatatcatctacctccgcaatgtgttgattgggttgttattattagaccattacttcactcta

Thau_2018_NSI_broyage_ind6_quasi-assembly_pilon_pilon gaaatgattgctgattggttga-------------------------------------------------------------------------------------------------------------------atgtgatatcatctacctccgcaatgtgttgattgggttgttattattagaccattacttcactcta

Region Ul-polyC

This region appears to be complex AAACACACACCCCCCCCCCCCCCAAACAAAGGGAAGATAACTCATGTGTTTTATAATTTTTTTATATTTATTTTTTTAAAAAAAAATAAAATCTATATATAGAACACACAAAAAAAATCATCATCATCACATCACATCATATTGGCAACGTCCCTATCGTAAAAGCAGTCCTTTCTCATGACGCTGGCAGAGCTCGACATGTCGCATCTGATGCACGCCTTGTACAGTCTCCTGATGTCCACCAGTCCCGTGTCTCCTATCTTGACTATCAATGGTTCTAGCAGCGTCTTTATGGTCTGTTTCTGCCTTTCGTGTTCCTCTTCATCGTAATCCGAGTCCCACGTGTTTATCCTGGGCGTGGAGGATATGTGTCTGTAGTCTTCAAACTTGCAATCGGGTTTGTAGAGCTTCACTTCCTCCACGAGTAGGTACAACTTCCTGGCGCTTCTCCTGCAAGCGTCTTCGACCAGGTGATACGAGACGTCGTTGGTGATCATGGGTTGACTGCCGTCTACCTCGGGAAGGTGTCTGTCCTTGTTTTTGATGCCAATGTCGTTTACCGCGGCCTTCTCCATGTCTTTGTCTCTCACCTTTTCTGTGAGTCTCTGATTGATGCGCCTCAATTCCGCCTTCTCGTCTTCCAGCACCACTATCCTCGCGGCCAGATCGTCCATTCGTTTATTCATCTCCGAAACCATATCGTCCATGGCGGTCTTTGCGTCCCTGGCGCGGTGCTCAAACATCTCCCTGACATTATGTTCGTGGGTGGTAACTTTGCTCGATAACCTCGTCACTTCAGTCTGCATAATGTTTATCCACATCGAGTCATTGGCAGTGGTGGTGGTGTTGTTACTGGCAGCAGCAATACCCTCTTCATTCATCTCCTCCTCATCATTCATCTCTTCCTCTTCACTGCAATGACTATCATCGTCGGCGTCAATGCCGCAGTAGCGGCAGTATGCATCACCACAATCGTAGGTATTCCAGCCCTAATCTTCTTCCGAGTCGCTGCTGCTCTGTAGTATGGCGTCGACCGGTGTACCTTCATTGTTATCCATTAGTTAATTGCGTGTGTTTTATGTAGTGCGTATGTGTGCGGGGGGGAGTTAAAGGCTTGTGTTCTAACACTGAGAGCAGATTTTGTATTTATATTACATGTCGCCCTTCCTTGGTAGTTCTTTGTTATGGGTGGTAATGAATATAATAATAACACTCTTGCCAATGTGTAAACCTGACATATCTGTATATACAAAAAACCATCTAATCACATCACACCAATGGATTTATGCTAATTTTGTTTATTCTAAAAATAACCATCCAATCAGATTGCTCGAGACCGATCTATCCTTTAGGATTTTGAGCTGGGGTAGATGCTCCGTGCTTGGGTCTATGGGGCTTGATGACTAATAACGGAGATTTAACACGGGGATGCGCATTACTAGGTATAAGTTGTAATGTTTATGCTATATTATGAACCTAGTTCCTTGGCCCCCCCCTTATGTGTAAGAGATAGATTGTAGTCTATTGCCAAGGTGTAGATAGAGATGTTTTTTGTTTAAACCATGTTAAAAAAATCTAACAATGCTATAAAGATCTCTATTATACAGTCGTACAAATCATTCAAGCTTAGCGAGACGATCTATAACAACCACACACACCAGAAAAAAACATGGAACATTTTACAGCGGAATGCATATTGGTAGACGAGAAATGCCACGTCATCGAAAGGCACGACATTGCCAAAGGTTCGTTGCAGACAGTTGCAGATCTACTGAGACACATTCACAGGTGGAAGACAGGGTGGTGAGAGCTTTGATGGAAGACGATGTCGATCTGTGGAGGAAGATGAAATACATGGTGATTAGCAGCAAGAATAATGACGATNNNNNNNNNNCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCAAA

I'm going to cut between the AAACACACA and the AAA

Overlaping reads used to confirmed sequence

> A00977:28:H2VGTDSXY:4:2673:26341:16047
AAGGAATTTCATCTTGCCAGGGAATTTTATTAAAACTTATTCCTTGCCGACCATCAATTCCTTGGCCAAAAAATGGTTTAAACCAAACACACACCCCCCCCCCCCCCAAACAAAGGGAAGATAACTCATGTGTTTTATAATTTTTTTATAT

From 4388 to 4534
Length: 147
Row: 149
Cigar: 93M4I54M
Strand: complement

-> AAACCAAACACACCCCCCCCCCCCCCCCCCCCCCAAA if the interest portion is restricted to the interest portion.

Sequence change code

export PATH=/appli/anaconda/3.7/bin/:$PATH
source activate seqkit
cd PATH/2020-04-29_final_genome
# Thau ind 6
genome=PATH/2020-04-28-asm_polish_2/Thau_2018_NSI_broyage_ind6_noPCR_asm_polished_contigs.fasta
echo -e ">Thau_2018_NSI_broyage_ind6_noPCR_NR-genome" > Thau_2018_NSI_broyage_ind6_noPCR_NR-genome.fasta
# permet de linéariser la séquence
seqkit seq --seq $genome | sed ':a;N;$!ba;s/\n//g' >> Thau_2018_NSI_broyage_ind6_noPCR_NR-genome.fasta
sed -i 's/GAAATGATTGCTGATTGGTTGAATGTGATATCATCTACCTCCGCAATGTGTTGATTGGGTTGTTATTATTAGACCATTACTTCACTCTA/GAAATGATTGCTGATTGGTTGAATGTGATATCATCTACCTCCGCAATGTGTTGATTGGGTTGTTATTATTAGACCATTACTTCACTCTAAAAATATAAACCAATGACTGTAGTCGGAAATGATTGCTGATTGGTTGAATGTGATATCATCTACCTCCGCAATGTGTTGATTGGGTTGTTATTATTAGACCATTACTTCACTCTA/' Thau_2018_NSI_broyage_ind6_noPCR_NR-genome.fasta

export PATH=/appli/anaconda/3.7/bin/:$PATH
source activate seqkit
cd 2020-04-29_final_genome
# Thau ind 6
genome=PATH/2020-04-28-asm_polish_2/Thau_2018_NSI_broyage_ind6_noPCR_asm_polished_contigs.fasta
echo -e ">Thau_2018_NSI_broyage_ind6_noPCR_NR-genome" > Thau_2018_NSI_broyage_ind6_noPCR_NR-genome.fasta
# permet de linéariser la séquence
seqkit seq --seq $genome | sed ':a;N;$!ba;s/\n//g' >> Thau_2018_NSI_broyage_ind6_noPCR_NR-genome.fasta
sed -i "s/AAACACACACCCCCCCCCCCCCCAAACAAAGGGAAGATAACTCATGTGTTTTATAATTTTTTTATATTTATTTTTTTAAAAAAAAATAAAATCTATATATAGAACACACAAAAAAAATCATCATCATCACATCACATCATATTGGCAACGTCCCTATCGTAAAAGCAGTCCTTTCTCATGACGCTGGCAGAGCTCGACATGTCGCATCTGATGCACGCCTTGTACAGTCTCCTGATGTCCACCAGTCCCGTGTCTCCTATCTTGACTATCAATGGTTCTAGCAGCGTCTTTATGGTCTGTTTCTGCCTTTCGTGTTCCTCTTCATCGTAATCCGAGTCCCACGTGTTTATCCTGGGCGTGGAGGATATGTGTCTGTAGTCTTCAAACTTGCAATCGGGTTTGTAGAGCTTCACTTCCTCCACGAGTAGGTACAACTTCCTGGCGCTTCTCCTGCAAGCGTCTTCGACCAGGTGATACGAGACGTCGTTGGTGATCATGGGTTGACTGCCGTCTACCTCGGGAAGGTGTCTGTCCTTGTTTTTGATGCCAATGTCGTTTACCGCGGCCTTCTCCATGTCTTTGTCTCTCACCTTTTCTGTGAGTCTCTGATTGATGCGCCTCAATTCCGCCTTCTCGTCTTCCAGCACCACTATCCTCGCGGCCAGATCGTCCATTCGTTTATTCATCTCCGAAACCATATCGTCCATGGCGGTCTTTGCGTCCCTGGCGCGGTGCTCAAACATCTCCCTGACATTATGTTCGTGGGTGGTAACTTTGCTCGATAACCTCGTCACTTCAGTCTGCATAATGTTTATCCACATCGAGTCATTGGCAGTGGTGGTGGTGTTGTTACTGGCAGCAGCAATACCCTCTTCATTCATCTCCTCCTCATCATTCATCTCTTCCTCTTCACTGCAATGACTATCATCGTCGGCGTCAATGCCGCAGTAGCGGCAGTATGCATCACCACAATCGTAGGTATTCCAGCCCTAATCTTCTTCCGAGTCGCTGCTGCTCTGTAGTATGGCGTCGACCGGTGTACCTTCATTGTTATCCATTAGTTAATTGCGTGTGTTTTATGTAGTGCGTATGTGTGCGGGGGGGAGTTAAAGGCTTGTGTTCTAACACTGAGAGCAGATTTTGTATTTATATTACATGTCGCCCTTCCTTGGTAGTTCTTTGTTATGGGTGGTAATGAATATAATAATAACACTCTTGCCAATGTGTAAACCTGACATATCTGTATATACAAAAAACCATCTAATCACATCACACCAATGGATTTATGCTAATTTTGTTTATTCTAAAAATAACCATCCAATCAGATTGCTCGAGACCGATCTATCCTTTAGGATTTTGAGCTGGGGTAGATGCTCCGTGCTTGGGTCTATGGGGCTTGATGACTAATAACGGAGATTTAACACGGGGATGCGCATTACTAGGTATAAGTTGTAATGTTTATGCTATATTATGAACCTAGTTCCTTGGCCCCCCCCTTATGTGTAAGAGATAGATTGTAGTCTATTGCCAAGGTGTAGATAGAGATGTTTTTTGTTTAAACCATGTTAAAAAAATCTAACAATGCTATAAAGATCTCTATTATACAGTCGTACAAATCATTCAAGCTTAGCGAGACGATCTATAACAACCACACACACCAGAAAAAAACATGGAACATTTTACAGCGGAATGCATATTGGTAGACGAGAAATGCCACGTCATCGAAAGGCACGACATTGCCAAAGGTTCGTTGCAGACAGTTGCAGATCTACTGAGACACATTCACAGGTGGAAGACAGGGTGGTGAGAGCTTTGATGGAAGACGATGTCGATCTGTGGAGGAAGATGAAATACATGGTGATTAGCAGCAAGAATAATGACGATNNNNNNNNNNCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCAAA/AAACACACACCCCCCCCCCCCCCAAA/" Thau_2018_NSI_broyage_ind6_noPCR_NR-genome.fasta
sed -i 's/GAAATGATTGCTGATTGGTTGAATGTGATATCATCTACCTCCGCAATGTGTTGATTGGGTTGTTATTATTAGACCATTACTTCACTCTA/GAAATGATTGCTGATTGGTTGAATGTGATATCATCTACCTCCGCAATGTGTTGATTGGGTTGTTATTATTAGACCATTACTTCACTCTAAAAATATAAACCAATGACTGTAGTCGGAAATGATTGCTGATTGGTTGAATGTGATATCATCTACCTCCGCAATGTGTTGATTGGGTTGTTATTATTAGACCATTACTTCACTCTA/' Thau_2018_NSI_broyage_ind6_noPCR_NR-genome.fasta

For the individual 4 LT 2018 the sequences that will be modified

Artifact: gatgtgtaatgatttgggtataggagattacttcgaattgatactcagnnnnnnnntgcacga

export PATH=/appli/anaconda/3.7/bin/:$PATH
source activate seqkit
cd /home1/datawork/jdelmott/2020-04-07-Metaviromic_Haplofit_backup/2020-04-29_final_genome
# LT ind 4
sed -i 's/GATGTGTAATGATTTGGGTATAGGAGATTACTTCGAATTGATACTCAGNNNNNNNNTGCACGA//' LT_2018_NSI_broyage_ind4_noPCR_NR-genome.fasta

Correction of polyN of other genome assemblages

SAMPLES CORRECTION
Brest_2018_NSI_broyage_ind10_noPCR TTATTAGACCATTACTTCACTCTAAAAATATAAACCAATGACTGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGGGTTGTTA
Brest_2018_NSI_broyage_ind2_noPCR TTATTAGACCATTACTTCACTCTAAAAATATAAACCAATGACTGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGGGTTGTTA
Brest_2018_NSI_broyage_ind4_noPCR TTATTAGACCATTACTTCACTCTAAAAATATAAACCAATGACTGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGGGTTGTTA
Brest_2018_NSI_broyage_ind6_noPCR TCTAAAAATATAAACCAATGACTGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
Brest_2018_NSI_broyage_ind9_noPCR TTATTAGACCATTACTTCACTCTAAAAATATAAACCAATGACTGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGGGTTGTTA
LT_2018_NSI_broyage_ind10_noPCR GACCATTACTTCACTCTAAAAATATAAACCAATGACTGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGGGTTGTTATTATTA
LT_2018_NSI_broyage_ind1_noPCR AACCAATGACTGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCTAAAAATATA
LT_2018_NSI_broyage_ind3_noPCR GNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGGGTTGTTATTATTAGACCATTACTTCACTCTAAAAATATAAACCAATGACT
LT_2018_NSI_broyage_ind4_noPCR ATGTGATATCATCTACCTCCGNNNNNNNNNNACCTGCCAAATACAGGATGTGCCCACCTCTTCTGATCAAGGTGCCAATTCAATACAGATTAGTGCCGCCCATAACAATCAGGAAGTGTGATCTGCCAATGGTTGAACTTGATAATGAACTATATATGTTTTTGGACAGTTATACTCCTCCTACCATGGAGGTCAATGGTGAATCTTATATGATAATTGACTCTTGTGATGCACCAACCATGAATATTAATGGAAAAACATATTATGTTATTGATGAATGTTAATTTTTTTTATTGATGAATGTTAATTTGTTGTTGTTTTATACTTGATTAAAAAAAAATGAAAATGAAGTAATATCTTTATTTATATTTTACATTGAAAACACACCCACCAAGGCGCAATCCAATAAAAATTGAGTATGGCCAGGTTAGAGTTCATGAACAATACAAATTGAGTATATTTGTACTTAGAAATTTTTCGCGCAAACCCCACAAACATATACTTTAACTTGAGATTTTTTTCTAAGTTGAAATTTTACATCATTGCGCATGTGTAAGGGAGAAACAAAATGGCGTAACAAAATGGCGGATTGTTCCCGCTATTTTATGAAACCACATTATAACGTATATTTTAAACCAATCATGTATCTACCATTGCTGCTGTTTTGCGTCATTTCCTGTTATGGTGAGCAGATAAACAACCTCGATGACCTCCAAGCAAAATTGGACAGCATGCCGCCCAGTGACTTTATTGACCACAATGGACATAATATATGCCAAGATTGCGACAGGTTATGTCCTTTAATTTCCGATAATCCCACATGTGAAGAAGATTGTTATGGGAGGTGTAACAAGGGGATAACACGGCAATGATTTAATTATTAATTCTATTTTTAAATATAACATCCAATGAAAACAGCCGGAAATTGTACCTGATTGATTTTTACCAATAAAAAAAATCAAAAGATAATGTATATTTTTTAGTATTTTTAATTTAAATTGTCAAATCAATATAGTCATCAATTATAATACAATCATCATCAATAGCATTGTTTACAGCAATATTGTCAATCATATCATTCATAAGTCTATCATTTGACATCTGCGACCTTTCGCTAAGCACCTCCTCCACCAAACTGTCCAATGTATAACGAGGAACATAATTGTCACTTTCATCATCACTAAGTAGGTGGTCTTCTTCCTCAGGTGTAAGTTCATCAATGTCATTATTATTCTCCAAAATCATGATATCATCATTGTCTATCAGCCAATACTTGTAGAGTTTAGCCTCATTTCCATAAATGATCCGCCTCTCCGGCCAGTCCTTTCTGCAGATTGGACACTTGTCTTCCATCTCCTGCCTTATGCAATTGTCACAAATGTAATGAGTTGGGCAGGGCATTGTCGTAACTCTCAATGCCCCTCCCTCAATGTCACATTCAGCCAATGTCTTTTTAGTATAAGTAGGCTCCATGCAGATAACACACACCTTCTCGACAGCATCAACTTTCGCCAACAATGTTTTTAATTTTCTGCCAGCCGCCATTGCTGTCTCTTTCGTCAGCTTCAACTTCTTAATCCCGCCCATGATCCTGGGTACGTCATGGACATGCGCAGTAGTAGTATTTCTGGACTTTACCATTTTCACAGCGTATTTTATATTCCTATATCTGCTAACAGTAGATGTGTACAGTAAGACTCCCAAGCAAGTTATGATTTTAACATGGGCAATAGCGCTGCTTATATAGAGCAGGCCAGGGTGCTGATTGGTCTGTTATTATTAGACCATTACATTTATTCTAAAAATATAAACCAATGACTGTAGTCGGAAATGATTGCTGATTGGTTGA
LT_2018_NSI_broyage_ind7_noPCR TGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCTAAAAATATAAACCAATGAC
LT_2018_NSI_broyage_ind8_noPCR CAATGACTGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGGGTTGTTATTATTAGACCATTACTTCACTCTAAAAATATAAAC
LT_2018_NSI_broyage_ind9_noPCR AACCAATGACTGNNNNNTTGGGTTGTTATTATTAGACCATTACTTCACTCTAAAAATATA
Thau_2018_NSI_broyage_ind10_noPCR GACCATTACTTCACTCTAAAAATATAAACCAATGACTGNNTTGGGTTGTTATTATTA
Thau_2018_NSI_broyage_ind4_noPCR GACCATTACTTCACTCTAAAAATATAAACCAATGACTGNTTGGGTTGTTATTATTA
Thau_2018_NSI_broyage_ind7_noPCR GACCATTACTTCACTCTAAAAATATAAACCAATGACTGNNNTTGGGTTGTTATTATTA

Sequence change code

#qsub -I -q omp -l walltime=05:00:00 -l mem=90g -l ncpus=8
export PATH=/appli/anaconda/3.7/bin/:$PATH
source activate seqkit
while read h f; do genome=PATH/2020-04-29_final_genome/${h}_NR-genome.fasta ; echo ">${h}_NR-genome" > $genome ; seqkit seq --seq PATH/2020-04-28-asm_polish_2/${h}_asm_polished_contigs.fasta | sed ':a;N;$!ba;s/\n//g' >> $genome ; sed -i "s/$f//" $genome ; done < OshV-1-molepidemio/raw/d-Manually_corrected_assembly/correction_polyN.csv

## Added des Thau_2018_NSI_broyage_ind8_noPCR Thau_2018_NSI_broyage_ind9_noPCR which was direct well assembled

genome=PATH/2020-04-28-asm_polish_2/Thau_2018_NSI_broyage_ind8_noPCR* 
echo -e ">Thau_2018_NSI_broyage_ind8_noPCR_NR-genome" > Thau_2018_NSI_broyage_ind8_noPCR_NR-genome.fasta
seqkit seq --seq $genome | sed ':a;N;$!ba;s/\n//g' >> Thau_2018_NSI_broyage_ind8_noPCR_NR-genome.fasta

genome=PATH/2020-04-28-asm_polish_2/Thau_2018_NSI_broyage_ind9_noPCR*
echo -e ">Thau_2018_NSI_broyage_ind9_noPCR_NR-genome" > Thau_2018_NSI_broyage_ind9_noPCR_NR-genome.fasta
seqkit seq --seq $genome | sed ':a;N;$!ba;s/\n//g' >> Thau_2018_NSI_broyage_ind9_noPCR_NR-genome.fasta