sra-toolkit

utilities for the NCBI Sequence Read Archive

Command lineScience

Install

Not tested on a device yet. What that means

Commands in the package

abi-load
align-cache
align-info
bam-load
cache-mgr
ccextract
cg-load
check-corrupt
check-redact
compute-coverage
compute-coverage-ngs
copycat
crc32sum
fastconv
fastq-load
general-loader
helicos-load
illumina-load
kar
kar+
kar+meta
kdb-index
kdbmeta
latf-load
make-read-filter
md5cp
meta-cmp
meta-copy
meta-repair
ngs-pileup
pacbio-correct
pacbio-load
pacbio-loadxml
pileup-stats
prefetch
rcexplain
read-filter-redact
ref-variation
rowwritetest
samview

And 28 more.

About sra-toolkit

From Debian's package description

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.
Other tools distributed in this package are: abi-dump, abi-load align-info bam-load cache-mgr cg-load copycat fasterq-dump fastq-dump, fastq-load helicos-load illumina-dump, illumina-load kar kdbmeta latf-load pacbio-load prefetch rcexplain remote-fuser sff-dump, sff-load sra-pileup, sra-sort, sra-stat, srapath srf-load test-sra vdb-config, vdb-copy, vdb-decrypt, vdb-encrypt, vdb-get, vdb-lock, vdb-passwd, vdb-unlock, vdb-validate
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.

From Debian's description of the sra-toolkit package, under that package's license.

Dependencies

Depends on

libabsl20240722
libbz2-1.0
libc6
libgcc-s1
libhdf5-310
libmagic1t64
libncbi-vdb3
libncbi-wvdb3
libre2-11-absl20240722
libstdc++6
libxml2
zlib1g

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Sources and licenses

Name: the Debian package name.
Summary: Debian's short description of the sra-toolkit package, under that package's license.
Description: Debian's description of the sra-toolkit package, under that package's license.
Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
Popularity: Debian Popularity Contest counts.