Download the public sequencing data using kingfisher

Kingfisher is quite convenient for us to download public sequencing data.

1. Install kingfisher

conda install -c conda-forge -c bioconda kingfisher # pay attention to the channel order

2. Examples of downloading date using kingfisher

kingfisher get -p PRJNA938179 -m aws-http prefetch aws-cp gcp-cp ena-ftp -f fastq --check-md5sums
kingfisher get -p PRJNA938179 -m aws-http prefetch aws-cp gcp-cp ena-ftp -t 16 -f fastq.gz --check-md5sums
kingfisher get -r SRR12044307 -m aws-http prefetch aws-cp gcp-cp ena-ftp -f fastq --check-md5sums
kingfisher get -r SRR12044307 -m aws-http prefetch aws-cp gcp-cp ena-ftp -t 16 -f fastq.gz --check-md5sums

kingfisher get --run-identifiers-list srr_list.txt -m aws-http prefetch aws-cp gcp-cp ena-ftp -t 16 -f fastq.gz --check-md5sums
srr_list.txt <
SRR12044304
SRR12044305
SRR12044306
SRR12044307
SRR12044308
SRR12044309

Appendix 1: aria2c

aria2c -c https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/020/567/875/GCA_020567875.1_IOCAS_Cari/GCA_020567875.1_IOCAS_Cari_genomic.fna.gz