SRR23410316 - Salmonella
ERR766214 - BCG
conda install bioconda::sra-tools
fasterq-dump -S ERR766214 # 2.2GB not compressed
wget
sra_number="ERR766214"
wget -O "${sra_number}.fastq.gz" "https://sra-pub-run-odp.s3.amazonaws.com/sra/${sra_number}/${sra_number}"
fasterq-dump -S ${sra_number}.fastq.gz
# faster than fasterq-dump, compressed - single FASTQ, then split
ENA browser tools downloads files as compressed but slower than wget
conda install bioconda::enabrowsertools # old
Download ENA at GitHub
sra_number="ERR766214"; enaDataGet --format fastq "$sra_number" # git pull if tool does not work to get the latest version.
List
ls -lh *fastq
View
head ERR766214_R1.fastq
Zip
pigz *fastq
List
ls -lh *fastq.gz
Add "R" for read
mv ERR766214_1.fastq.gz ERR766214_R1.fastq.gz
mv ERR766214_2.fastq.gz ERR766214_R2.fastq.gz
Get stats using SeqKit
seqkit stats *.fastq.gz -T > out.tab
Simple search
seqkit grep -s -m 1 -p "ATGGCGGGGTCA" *gz -C
Parse sequence
seqkit grep -s -m 1 -p "ATGGCGGGGTCA" *_R1*gz > found_sequence_R1.fastq
Assembly
spades.py -1 *_R1*fastq.gz -2 *_R2*fastq.gz -o spades_assembly
If SPAdes fails download binaries and add bin to your PATH
PATH=$PATH:${HOME}/SPAdes-3.15.5-Darwin/bin
which spades.py
PATH=${HOME}/SPAdes-3.15.5-Darwin/bin:$PATH
vsnp3_assembly.py -f ./spades_assembly/scaffolds.fasta
View head ./spades_assembly/scaffolds.fasta
vsnp3_fastq_stats_seqkit.py -r1 ERR766214_R1.fastq.gz -r2 ERR766214_R2.fastq.gz
fastqc ERR766214_R1.fastq.gz ERR766214_R2.fastq.gz