1.1 fastq-dl

Installation
One way to install fastq-dl is via conda from the Bioconda channel. By following the commands below, you will set up a conda environmental called fastq-dl which downloads fastq-dl and all of its dependencies to the fastq-dl environment.

conda create -n fastq-dl -c conda-forge -c bioconda fastq-dl
conda activate fastq-dl

Note: installing via conda requires you to have installed miniconda3 or miniforge3

Tip: to deactivate a conda environment type conda activate base

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Download reads
Download raw reads for a single sequencing run to the current working directory.

# Download from the SRA
fastq-dl --outdir . --cpus 4 SRR18391668 SRA

# Download from the ENA
fastq-dl --outdir . --cpus 4 SRR18391668 ENA

Note: for paired reads, the fastq-dl default is to download two separate gzipped FASTQ files

You can also specify a project or experiment accession ID. For example, supplying the project accession, PRJNA804719, tells the program to download all 136 sequencing runs to the current directory. Similarly, supplying the experiment accession, SRX14525734, tells the program to download all sequencing runs for that experiment. In the example used here, there is only one run in the experiment so only one sample of paired reads will be downloaded.

# Download all sequencing experiments for Project PRJNA804719
fastq-dl --outdir . --cpus 4 PRJNA804719 SRA # SRA
fastq-dl --outdir . --cpus 4 PRJNA804719 ENA # ENA

# Download all sequencing runs for Experiment SRX14525734
fastq-dl --outdir . --cpus 4 SRX14525734 SRA # SRA
fastq-dl --outdir . --cpus 4 SRX14525734 ENA # ENA

*Note: to download all 136 sequencing runs you will need approximately 20GB storage space

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2.1 Nucleotide

Single 16S rRNA sequence
Download the AF276989 16S rRNA sequence for Salmonella enterica in FASTA format.

efetch -db nucleotide -id AF276989 -format fasta > AF276989_16S.fa

Multiple 16S rRNA sequences
Download multiple 16S rRNA sequences for Salmonella enterica in FASTA format.

efetch -db nucleotide -id AF276989,NR_074799,NR_041696,NR_074910,NR_119108 -format fasta > Senterica_16S.fa

Multiple 16S rRNA sequences — text file containing IDs
Same as above but instead submit a text file containing the IDs to download.

# Text file called nucleotide_ids.txt
AF276989
NR_074799
NR_041696
NR_074910
NR_119108

efetch -db nucleotide -input nucleotide_ids.txt -format fasta > Senterica_16S.fa

Mitogenome
Download the complete mitochondrion genome (MH747083) for Homarus gammarus in FASTA format.

efetch -db nucleotide -id MH747083 -format fasta > Hgammarus_mitogenome.fa

Plastome
Download the complete plastid genome (MH281627) for Lithothamnion sp. in FASTA format.

efetch -db nucleotide -id MH281627 -format fasta > LithothamnionSp_plastome.fa

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2.2 Protein

Single protein sequence
Download the NP_776541 protein sequence for myogenic factor 5 (Bos taurus) in FASTA format.

efetch -db protein -id NP_776541 -format fasta > Btaurus_MYF5.fa

Multiple protein sequences
Download multiple protein sequences for humans in FASTA format.

efetch -db protein -id NP_001186746,AAB51177,AAB51171,AAF88103,AAF88103 -format fasta > Human_proteins.fa

Multiple protein sequences — text file containing IDs
Same as above but instead submit a text file containing the IDs to download.

# Text file called protein_ids.txt
NP_001186746
AAB51177
AAB51171
AAF88103
AAF88103

efetch -db protein -input protein_ids.txt -format fasta > Human_proteins.fa

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2.3 Gene

Single gene
Download information for the Mbis1 gene (492906) from mouse (Mus musculus) in tabular format.

# Method 1: use gene ID
efetch -db gene -id 492906 -format tabular > Mouse_Mbis1.tsv

# Method 2: use a descriptive query
esearch -db gene -query "Mus musculus Mbis1" | efetch -format tabular > Mouse_Mbis1.tsv

Multiple genes
Download information for multiple genes from zebrafish (Danio rerio) in tabular format.

efetch -db gene -id 30592,30513,30425,30590,30269 -format tabular > Zebrafish_genes.tsv

Multiple genes — text file containing IDs
Same as above but instead submit a text file containing the IDs to download.

# Text file called gene_ids.txt
30592
30513
30425
30590
30269

efetch -db gene -input gene_ids.txt -format tabular > Zebrafish_genes.tsv

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2.4 Assembly

Mycobacterium bovis
Download Mycobacterium bovis complete genome assembly (GCA_005156105.1) in gzipped FASTA format.

wget $(esearch -db assembly -query "GCA_005156105.1" | esummary | xtract -pattern DocumentSummary -element FtpPath_RefSeq | awk -F"/" '{print $0"/"$NF"_genomic.fna.gz"}')

Homarus americanus
Download Homarus americanus scaffold genome assembly (GCA_018991925.1) in gzipped FASTA format.

wget $(esearch -db assembly -query "GCA_018991925.1" | esummary | xtract -pattern DocumentSummary -element FtpPath_RefSeq | awk -F"/" '{print $0"/"$NF"_genomic.fna.gz"}')

Chondrus crispus
Download Chondrus crispus scaffold genome assembly (GCA_000350225.2) in gzipped FASTA format.

wget $(esearch -db assembly -query "GCA_000350225.2" | esummary | xtract -pattern DocumentSummary -element FtpPath_RefSeq | awk -F"/" '{print $0"/"$NF"_genomic.fna.gz"}')

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Further information for downloading data via EDirect can be found on the following pages:

https://www.ncbi.nlm.nih.gov/books/NBK179288/
https://github.com/NCBI-Hackathons/EDirectCookbook