install_aspera_connect

Установите последнюю версию Aspera Connect (Linux 64-бит).

Установка

 # Clone this repository.
git clone https://github.com/aertslab/install_aspera_connect

cd install_aspera_connect

# Install latest version of Aspera Connect (linux 64-bit).
./install_aspera_connect.sh

Aspera Connect теперь доступен:

 ~/.aspera/connect/bin/ascp

Убедитесь, что порт 33001 TCP и UDP открыты и доступны из Интернета на машине, с которой вы запускаете Aspera Connect, иначе вы увидите такую ​​ошибку, подобную этой:

 Session Stop  (Error: Client unable to connect to server (check UDP port and firewall))

Aspera Connect Documentation

Aspera Connect Documentation

Скачать данные секвенирования

Архив чтения последовательности (SRA) / Экспрессия гена Omnibus (GEO)

 # Download SRA file directly with ascp:
~ /.aspera/connect/bin/ascp 
    -i ~ /.aspera/connect/etc/asperaweb_id_dsa.openssh 
    -pQTk1 
    -l 1000m 
    [email protected]:data/sracloud/traces/sra46/SRR/005227/SRR5353377 
    SRR5353377.sra

# Convert SRA file to gzipped FASTQ files with fastq-dump (SRA toolkit).
fastq-dump --gzip --split-files SRR5353377.sra

# Convert SRA file to FASTQ with fasterq-dump (SRA toolkit) and compress FASTQ files with gzip.
fasterq-dump --split-files SRR5353377.sra
gzip SRR5353377_1.fastq
gzip SRR5353377_2.fastq

Загрузка данных с сайта SRA

Загрузите файл SRA с помощью Prefetch (из SRA Toolkit, который использует ASCP ( -t fasp )

 # Use prefetch (SRA toolkit) to download SRA file:
#   - SRA files will be written to: $HOME/ncbi/public/sra/
#   - If your HOME dir is constrained in space, make a symlink:
#       ln -s /dir_with_lots_of_free_space/ncbi ${HOME}/ncbi
prefetch -v -t fasp SRR5353377

# Convert SRA file to gzipped FASTQ files with fastq-dump (SRA toolkit).
fastq-dump --gzip --split-files SRR5353377

# Convert SRA file to FASTQ with fasterq-dump (SRA toolkit) and compress FASTQ files with gzip.
fasterq-dump --split-files SRR5353377
gzip SRR5353377_1.fastq
gzip SRR5353377_2.fastq

1000 геномов проект

 ~ /.aspera/connect/bin/ascp 
    -i ~ /.aspera/connect/etc/asperaweb_id_dsa.openssh 
    -Tr 
    -Q 
    -l 100M 
    -P33001 
    -L- 
    [email protected]:vol1/ftp/release/20100804/ALL.2of4intersection.20100804.genotypes.vcf.gz ./

http://www.internationalgenome.org/faq/how-download-files-using-aspera/)

Европейский нуклеотидный архив (ENA)

ascp -QT -l 300m -P33001 -i /etc/aperaweb_id_dsa.openssh [email protected]:/vol1/ERA012/ERA012008/sff/library08_GJ6U61T06.sff .
~ /.aspera/connect/bin/ascp 
    -i ~ /.aspera/connect/etc/asperaweb_id_dsa.openssh 
    -QT 
    -l 300m 
    -P33001 
    [email protected]:vol1/ftp/release/20100804/ALL.2of4intersection.20100804.genotypes.vcf.gz ./

https://www.ebi.ac.uk/ena/browse/read-download#downloading_files_aspera