kilaza/amw

16S analysis tutorial - part of Analysing the Microbiome Workshop 2017. We ran this on the Wits cluster.

16S analysis tutorial - part of Analysing the Microbiome Workshop 2017

The dataset

The dataset we will be working are the practice dataset from the H3ABioNet 16S rDNA diversity analysis SOP. The source data can be accessed here but for our purposes it is already on the cluster and stored here:/local/mb/dog_stool_samples

The table below contains the metadata associated with the dog stool samples. There are three dogs which are treated with increased percentage of a compound in their diet: 5 different treatments (0-4, representing an increased percentage of a compound in their diet).

Sample	Dog	Treatment	Read counts r1	Read counts r2
Dog1	B	2	118343	118343
Dog2	G	3	108679	108679
Dog3	K	3	101482	101482
Dog8	B	4	108731	108731
Dog9	G	0	109500	109500
Dog10	K	4	79342	79342
Dog15	B	1	131483	131483
Dog16	G	4	114424	114424
Dog17	K	0	99610	99610
Dog22	B	3	145029	145029
Dog23	G	1	193158	193158
Dog24	K	2	162487	162487
Dog29	B	0	122776	122776
Dog30	G	2	137315	137315
Dog31	K	1	150613	150613

Outcomes

• Edit files and command line options, work with bash variables, use bash snippets (pipes, awk, loops).
• Run a 16S analysis pipeline from raw reads up to OTU classification and alignment.
• Once done with this tutorial you can continue with the R downstream analysis tutorial using the data generated in this tutorial.

Do some local setup

Setup some PATHS

export PATH=$PATH:/global/mb/amw/soft/fasta-splitter-0.2.4
export PATH=/global/mb/amw/soft/ImageMagick-7.0.5-3/install/bin:$PATH
export PATH=$PATH:/global/mb/amw/soft/amw-src
export PATH=$PATH:/global/mb/amw/soft/amw-src/fastqc_combine

Setup some directory and database variables

Be sure you have created ad temporary directory for yourself

mkdir /tmp/gerrit (here you need to set the name to your username)

Now set some variables.

raw_reads_dir=/local/mb/dog_stool_samples
process_dir=/tmp/gerrit (here you need to change it to the temporary directory you have created)
uparse_dir=$process_dir/uparse
taxonomy_dir=$process_dir/tax
alignment_dir=$process_dir/align
greengenes_db=/global/mb/amw/dbs/gg_13_8_otus
gold_db=/global/mb/amw/dbs/gold.fa
sid_fastq_pair_list=/global/mb/amw/sid.fastq_pair.list

Tutorial pipeline

When you get lost or something is unclear

1. All the outputs have been generated here /global/mb/amw/run
2. Please find someone next to you that looks like they know what they are doing.
3. Let me know.

1. Lets do some QC on the raw data

To be able to run all tools in the tutorial be sure these modules are loaded

module load bioinf
module load microbiome

1.1 Run FastQC

fastqc_dir=$process_dir/fastqc
mkdir $fastqc_dir
fastqc --extract -f fastq -o $fastqc_dir -t 6 $raw_reads_dir/*

1.2 Combine FastQC reports

fastqc_combine.pl -v --out $fastqc_dir --skip --files "$fastqc_dir/*_fastqc"

Now lets view the reports.

2. Run the UPARSE pipeline

2.1 First rename the read headers so that they are compatible with the UPARSE pipline

renamed_dir=$uparse_dir"/renamed"
mkdir -p $renamed_dir
while read sid_fastq_pair; do sid=`echo $sid_fastq_pair | awk -F ' ' '{print $1}'`; fastq_r1=`echo $sid_fastq_pair | awk -F ' ' '{print $2}'`; fastq_r2=`echo $sid_fastq_pair | awk -F ' ' '{print $3}'`; fastq_r1_renamed=$renamed_dir"/"$(basename $fastq_r1); fastq_r2_renamed=$renamed_dir"/"$(basename $fastq_r2); rename_fastq_headers.sh $sid $fastq_r1 $fastq_r2 $fastq_r1_renamed $fastq_r2_renamed;done < $sid_fastq_pair_list

This will take about 10 minutes to run. Lets have a look at the headers once done.

2.2 Merge the paired reads

fastq_maxdiffs=3
merged_dir=$uparse_dir"/merged"
mkdir $merged_dir

while read sid_fastq_pair; do sid=`echo $sid_fastq_pair | awk -F ' ' '{print $1}'`; fastq_r1=`echo $sid_fastq_pair | awk -F ' ' '{print $2}'`; fastq_r2=`echo $sid_fastq_pair | awk -F ' ' '{print $3}'`; fastq_r1_renamed=$renamed_dir"/"$(basename $fastq_r1); fastq_r2_renamed=$renamed_dir"/"$(basename $fastq_r2); usearch -fastq_mergepairs $fastq_r1_renamed -reverse $fastq_r2_renamed -fastq_maxdiffs $fastq_maxdiffs -fastqout $merged_dir"/"$sid".merged.fastq";done < $sid_fastq_pair_list

This will take about 1 minute to run. Lets have a look at the fastq files of the merge reads.

2.3 Filter

fastq_maxee=0.1
filtered_dir=$uparse_dir"/filtered"
mkdir $filtered_dir

while read sid_fastq_pair; do sid=`echo $sid_fastq_pair | awk -F ' ' '{print $1}'`;  usearch -fastq_filter $merged_dir"/"$sid".merged.fastq" -fastq_maxee $fastq_maxee -fastqout $filtered_dir"/"$sid".merged.filtered.fastq"  ;done < $sid_fastq_pair_list

This will take about 1 minute to run. Lets do a read count on the filtered fastqs.

2.4 Run FastQC on the filtered reads

filtered_fastqc_dir=$uparse_dir"/filtered.fastqc"
mkdir $filtered_fastqc_dir
fastqc --extract -f fastq -o $uparse_dir"/filtered.fastqc" -t 6 $filtered_dir/*.fastq

This will take about 2 minutes to run.

2.5 Combine FastQC reports

fastqc_combine.pl -v --out $filtered_fastqc_dir --skip --files "$filtered_fastqc_dir/*_fastqc"

Lets have a look at the FastQC summaries and see if we notice any changes from the FastQC reports on the raw reads.

2.6 Convert Fastq to Fasta

filtered_fasta_dir=$uparse_dir"/filtered.fasta"
mkdir $filtered_fasta_dir
for i in `ls -1 $filtered_dir/*.fastq`; do filename=$(basename "$i"); base="${filename%.*}"; seqtk seq -A $i > $filtered_fasta_dir/$base.fa; done

Lets have a look at the fasta format.

2.7 Do dereplication

cat $filtered_fasta_dir/*.fa > $uparse_dir/filtered_all.fa

cat $uparse_dir/filtered_all.fa | grep -v "^>" | grep -v [^ACGTacgt] | sort -d | uniq -c | while read abundance sequence ; do hash=$(printf "${sequence}" | sha1sum); hash=${hash:0:40};printf ">%s;size=%d;\n%s\n" "${hash}" "${abundance}" "${sequence}"; done > $uparse_dir/filtered_all.uniques.fa 2> $uparse_dir/filtered_all.uniques.fa.e

This will take about 15 minutes. Lets have a look at the headers.

2.8 OTU picking

Sort by size

min_size=2
usearch -sortbysize $uparse_dir/filtered_all.uniques.fa -fastaout $uparse_dir/filtered_all.uniques.sorted.fa -minsize $min_size

Do OTU picking

otu_radius_pct=3
usearch -cluster_otus $uparse_dir/filtered_all.uniques.sorted.fa -otu_radius_pct $otu_radius_pct -otus $uparse_dir/otus_raw.fa

This will take about 30 seconds. Once done lets count how many OTUs were generated.

2.9 Chimera removal

usearch -uchime2_ref $uparse_dir/otus_raw.fa -db $gold_db -mode high_confidence -strand plus -notmatched $uparse_dir/otus_chimOUT.fa

This will take about 10 seconds. Once done lets check how many OTUs were detected as being chimeric.

2.10 De-dereplication

Rename OTU headers

fasta_number.py $uparse_dir/otus_chimOUT.fa OTU_ > $uparse_dir/otus_repsetOUT.fa

Split fasta files to reduce memory on usearch_global run

mkdir $uparse_dir/split_files
fasta-splitter.pl --n-parts 100 --out-dir $uparse_dir/split_files/ $uparse_dir/filtered_all.fa

Do de-dereplication

for i in $(ls $uparse_dir/split_files/*.fa); do usearch -usearch_global $i -db $uparse_dir/otus_repsetOUT.fa -id 0.97 -strand plus -uc $i.map.uc; done

Combine mappings

cat $uparse_dir/split_files/*.map.uc > $uparse_dir/otus_mappedOUT.uc

This will take about 1 minute to complete. Lets have a look at the final mapping file.

2.11 Create QIIME compatible OTU table

uc2otutab.py $uparse_dir/otus_mappedOUT.uc > $uparse_dir/otus_table.tab.txt

This will take about 20 seconds to complete. Have a look that the OTU table generated.

2.12 Assign taxonomy

mkdir $taxonomy_dir
assign_taxonomy.py -i $uparse_dir/otus_repsetOUT.fa -o $taxonomy_dir -r $greengenes_db/rep_set/97_otus.fasta -t $greengenes_db/taxonomy/97_otu_taxonomy.txt -m uclust

This will take about a minutee to complete. Let look at the GreenGenes files and also the final output.

For downstream analysis we need a .biom file. Lets create that from the OTU table.

biom convert -i $uparse_dir/otus_table.tab.txt --table-type="OTU table" --to-json -o $process_dir/otus_table.biom

Now lets add the taxonomy annotation to the .biom file.

biom add-metadata -i $process_dir/otus_table.biom -o $process_dir/otus_table.tax.biom --observation-metadata-fp $taxonomy_dir/otus_repsetOUT_tax_assignments.txt --observation-header OTUID,taxonomy,confidence --sc-separated taxonomy --float-fields confidence --output-as-json

Lets have a look if the annotation has been added.

2.13 Create phylogenetic tree

Allign sequences against a template database

mkdir $alignment_dir
align_seqs.py -m pynast -i $uparse_dir/otus_repsetOUT.fa -o $alignment_dir -t $greengenes_db/rep_set_aligned/97_otus.fasta

This will take about 5 minutes to complete. Have a look at the output.

Now filter the alignment to remove gaps.

filter_alignment.py -i $alignment_dir/otus_repsetOUT_aligned.fasta -o $alignment_dir/filtered

Create a phylogenetic tree

make_phylogeny.py -i $alignment_dir/filtered/otus_repsetOUT_aligned_pfiltered.fasta -o $process_dir/otus_repsetOUT_aligned_pfiltered.tre

2.14 Create some summaries

biom summarize-table -i $process_dir/otus_table.tax.biom -o $process_dir/otus_table.tax.biom.summary.quantative

biom summarize-table --qualitative -i $process_dir/otus_table.tax.biom -o $process_dir/otus_table.tax.biom.summary.qualitative

Software needed to run this tutorial

• FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
• ImageMagick (https://www.imagemagick.org/script/download.php)
• Fastx-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/)
• Fasta-splitter (http://kirill-kryukov.com/study/tools/fasta-splitter/files/fasta-splitter-0.2.4.zip)
• USEARCH (http://www.drive5.com/usearch/download.html)
• UPARSE helper scripts (http://drive5.com/python/python_scripts.tar.gz)
• QIIME base (http://qiime.org/install/alternative.html)