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.
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.
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'
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).
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 ${bamfile}_sort.bam
We observed (see below) that there were no reads that could cross this ployN.
Then we looked at how to align the reads in this region (560bp) of the OsHV-1 µVar A genome.
while read h f; do r1=`ls /PATH/OshV-1-molepidemio/raw/${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.
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.
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).
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
Example of Thau_2018_NSI_broyage_ind3_noPCR
Thau_2018_NSI_broyage_ind1_quasi-assembly_pilon_pilon cggaaatgattgctgattggttga-------------------------------------------------------------------------------------------------------------------atgtgatatcatctacctccgcaat
NR-genome_Ostreid_herpesvirus_1_strain_microVar_variant_A cggaaatgattgctgattggttgaatgtgatatcatctacctccgcaatgtgttgattgggttgttattattagaccattacttcactctaaaaatataaaccaatgactgtagtcggaaatgattgctgattggttgaatgtgatatcatctacctccgcaat
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.
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
NR-genome_Ostreid_herpesvirus_1_strain_microVar_variant_B tcggaaatgattgctgattggttgaatgtgatatcatctacctccgcaatgtgttgattgggttgttattattagaccattacttcactctaaaaatataaacca
Thau_2018_NSI_broyage_ind3_quasi-assembly_pilon_pilon tcggaaatgattgctgattggttgaatg----------------------nnnnnnnttgggttgttattattagaccattacttcactctaaaaatataaacca
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.
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
NR-genome_Ostreid_herpesvirus_1_strain_microVar_variant_B tgctgattggtctgttattattagaccattacatttattctaaaaatataaaccaatgactgtagtcggaaatgattgctgattggttgaatgtgatatcatctacctccgcaatgtgttgattgggttgttattattagaccattacttcactctaaaaatataaaccaatgactgtagtcggaaatg
Thau_2018_NSI_broyage_ind5_quasi-assembly_pilon_pilon tgctgattggtctgttattattagaccattacatttattctaaaaatataa-------------------------------------------------------------------------------------------------------------------accaatgactgtagtcggaaatg
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
NR-genome_Ostreid_herpesvirus_1_strain_microVar_variant_B gaaatgattgctgattggttgaatgtgatatcatctacctccgcaatgtgttgattgggttgttattattagaccattacttcactctaaaaatataaaccaatgactgtagtcggaaatgattgctgattggttgaatgtgatatcatctacctccgcaatgtgttgattgggttgttattattagaccattacttcactcta
Thau_2018_NSI_broyage_ind6_quasi-assembly_pilon_pilon gaaatgattgctgattggttga-------------------------------------------------------------------------------------------------------------------atgtgatatcatctacctccgcaatgtgttgattgggttgttattattagaccattacttcactcta
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.
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
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
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 |
#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