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Last pushed: 4 months ago
Short Description
Sratoolkit 2.5.7 + aspera-connect 3.6.2
Full Description

This container contains the tools:

  • sratoolkit
  • aspera-connect

To download a sra file (SRR628588.sra for example) :

docker run -v $PWD:/mnt -ti flemoine/sratoolkit \
   /bin/bash -c 'ascp -i $ASCPKEY -k 1 -T -l300m \
   anonftp@ftp.ncbi.nlm.nih.gov:/sra/sra-instant/reads/ByRun/sra/SRR/SRR628/SRR628588/SRR628588.sra /mnt/'

To convert the sra file into two Fastq files

docker run -v $PWD:/mnt -ti flemoine/sratoolkit /bin/bash -c \
    'fastq-dump --gzip --split-files /mnt/SRR628588.sra -O /mnt/'
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flemoine
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