12. Coding solutions¶
12.1. QC¶
12.1.1. Code: Sickle¶
# run sickle like this on the ancestor:
sickle pe -g -t sanger -f data/ancestor-R1.fastq.gz -r data/ancestor-R2.fastq.gz -o trimmed/ancestor-R1.trimmed.fastq.gz -p trimmed/ancestor-R2.trimmed.fastq.gz -s trimmed/ancestor-singles.fastq.gz
# run the evolved samples through sickle
sickle pe -g -t sanger -f data/evolved-6-R1.fastq.gz -r data/evolved-6-R2.fastq.gz -o trimmed/evolved-6-R1.trimmed.fastq.gz -p trimmed/evolved-6-R2.trimmed.fastq.gz -s trimmed/evolved-6-singles.fastq.gz
12.1.2. Code: FastQC¶
Create directory:
mkdir trimmed-fastqc
Run FastQC:
fastqc -o trimmed-fastqc trimmed/ancestor-R1.trimmed.fastq.gz trimmed/ancestor-R2.trimmed.fastq.gz trimmed/evolved-6-R1.trimmed.fastq.gz trimmed/evolved-6-R2.trimmed.fastq.gz
Open html webpages:
firefox trimmed-fastqc/\*.html
12.2. Assembly¶
12.2.1. Code: SPAdes assembly (trimmed data)¶
spades.py -o assembly/spades-150/ -k 21,33,55,77 --careful -1 trimmed/ancestor-R1.trimmed.fastq.gz -2 trimmed/ancestor-R2.trimmed.fastq.gz
12.2.2. Code: SPAdes assembly (original data)¶
spades.py -o assembly/spades-original/ -k 21,33,55,77 --careful -1 data/ancestor-R1.fastq.gz -2 data/ancestor-R2.fastq.gz
12.3. Mapping¶
12.3.1. Code: Bowtie2 indexing¶
Build the index:
bowtie2-build assembly/spades_final/scaffolds.fasta assembly/spades_final/scaffolds
12.3.2. Code: Bowtie2 mapping¶
Map to the genome. Use a max fragemnt length of 1000 bp:
bowtie2 -X 1000 -x assembly/spades_final/scaffolds -1 trimmed/evolved-6-R1.trimmed.fsatq.gz -2 trimmed/evolved-6-R2.trimmed.fastq.gz -S mappings/evolved-6.sam
12.3.3. Code: BWA indexing¶
Index the genome assembly:
bwa index assembly/spades_final/scaffolds.fasta
12.3.4. Code: BWA mapping¶
Run bwa mem:
# trimmed data
bwa mem assembly/spades_final/scaffolds.fasta trimmed/evolved-6-R1.trimmed.fastq.gz trimmed/evolved-6-R2.trimmed.fastq.gz > mappings/evolved-6.sam
# raw data
bwa mem assembly/spades_final/scaffolds.fasta data/evolved-6-R1.fastq.gz data/evolved-6-R2.fastq.gz > mappings/evolved-6.raw.sam