Sequencing Results
2018
Week 1
MiSeq Quality scores
1
2
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5
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39
40
Week 2
MiSeq Quality scores
1
2
3
4
5
6
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10
11
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20
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31
32
33
34
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37
Week 3
MiSeq Quality scores
1
2
3
4
5
6
7
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9
10
11
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14
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18
19
20
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32
33
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36
Week 4
MiSeq Quality scores
1
2
3
4
5
6
7
8
9
10
11
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14
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18
19
20
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32
33
34
35
Week 5
MiSeq Quality scores
1
2
3
4
5
6
7
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10
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18
19
20
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36
Week 6
MiSeq Quality scores
1
2
3
4
5
6
7
8
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10
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18
19
20
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33
34
Week 7
MiSeq Quality scores
1
2
3
4
5
6
7
8
9
10
11
12
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14
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16
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18
19
20
21
22
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31
32
33
34
35
36
Week 8
MiSeq Quality scores
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
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25
26
27
28
29
30
31
32
33
34
35
36
Week 9
MiSeq Quality scores
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
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25
26
27
28
29
30
31
32
33
34
35
Week 10
MiSeq Quality scores
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
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25
26
27
28
29
30
31
32
33
34
35
36
Week 11
MiSeq Quality scores
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
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25
26
27
28
29
30
31
32
33
34
35
36
Week 12
MiSeq Quality scores
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
Week 13
MiSeq Quality scores
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
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28
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30
31
32
33
34
35
36
Week 14
MiSeq Quality scores
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
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27
28
29
30
31
32
33
34
35
36
Week 15
MiSeq Quality scores
1
2
3
4
5
6
7
8
9
10
11
12
13
14
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18
19
20
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36
2019
Week 1
MiSeq Quality scores
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
Week 2
MiSeq Quality scores
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
Week 3
MiSeq Quality scores
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
Week 4
MiSeq Quality scores
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
Week 5
MiSeq Quality scores
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
Week 6
MiSeq Quality scores
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
Week 7
MiSeq Quality scores
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
Week 8
MiSeq Quality scores
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
Week 9
MiSeq Quality scores
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
Week 10
MiSeq Quality scores
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
Week 11
MiSeq Quality scores
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
Week 12
MiSeq Quality scores
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
Week 13
MiSeq Quality scores
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
Week 14
MiSeq Quality scores
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
Week 15
MiSeq Quality scores
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
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29
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31
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35
36
Read Processing Pipeline
for file in $(ls ../data/raw_reads/2018/1-*_L001_R1_001.fastq)
do \
directory=$(dirname "$file")
sample="$(basename -- $file)"
sample=$(echo "$sample" | cut -f 1 -d '.')
sample=$(echo "$sample" | sed s/'_L001_R1_001'//g)
sample=$(echo "$sample" | cut -f 1 -d '_')
mikdir -p ${directory}/../assembled/../error_files/../clustered/../finalized_reads/../classifiedMerge Paired-End Reads
pear \
-j 8 \
-p 0.05 \
-v 10 \
-n 225 \
-m 290 \
-f ${file} \
-r ${directory}/${sample}*_R2_* \
-o ${directory}/../assembled/${sample}Trimming
cutadapt \
-l 225 \
-m 225 \
-o ${directory}/../assembled/${sample}.assembled.trimmed.fastq \
${directory}/../assembled/${sample}.assembled.fastqASV Calling
amplici \
--fastq ${directory}/../assembled/${sample}.assembled.trimmed.fastq \
--outfile ${directory}/../error_files/${sample}.error \
-error
amplici \
--fastq ${directory}/../assembled/${sample}.assembled.trimmed.fastq \
--profile ${directory}/../error_files/${sample}.error \
--outfile ${directory}/../clustered/${sample}.fastaChimera Removal
vsearch-2.15.1/bin/vsearch \
--sortbysize ${directory}/../clustered/${sample}.fasta \
--output ${directory}/../clustered/${sample}.sorted.fasta
vsearch-2.15.1/bin/vsearch \
--uchime_denovo ${directory}/../clustered/${sample}.sorted.fasta \
--nonchimeras ${directory}/../finalized_reads/${sample}.nonchimeras.fastaClassifier
java -Xmx24g -jar /mnt/home/smithsch/software/RDPTools/classifier.jar \
classify \
-c 0.5 \
-f filterbyconf \
-o ${directory}/../classified/${sample}_classifications.txt \
${directory}/../finalized_reads/${sample}.nonchimeras.fasta
done
Schuyler Smith
Ph.D. Student - Bioinformatics and Computational Biology
Iowa State University. Ames, IA.