sam-dump
utilities for the NCBI Sequence Read Archive
Install
- All systems
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curl cmd.cat/sam-dump.sh
- Debian
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apt-get install sra-toolkit - Ubuntu
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apt-get install sra-toolkit - Kali Linux
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apt-get install sra-toolkit - Windows (WSL2)
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sudo apt-get updatesudo apt-get install sra-toolkit - Dockerfile
- dockerfile.run/sam-dump
sra-toolkit
utilities for the NCBI Sequence Read Archive
Tools for reading the SRA archive, generally by converting individual runs into some commonly used format such as fastq. The textual dumpers "sra-dump" and "vdb-dump" are provided in this release as an aid in visual inspection. It is likely that their actual output formatting will be changed in the near future to a stricter, more formalized representation[s]. PLEASE DO NOT RELY UPON THE OUTPUT FORMAT SEEN IN THIS RELEASE. The "help" information will be improved in near future releases, and the tool options will become standardized across the set. More documentation will also be provided documentation on the NCBI web site. Tool options may change in the next release. Version 1 tool options will remain supported wherever possible in order to preserve operation of any existing scripts.