Rasusa: Randomly subsample sequencing reads to a specified coverage

Rasusa: Randomly subsample sequencing reads to a specified coverage - Published in JOSS (2022)
https://github.com/mbhall88/rasusa

Keywords

alignment bam bioinformatics coverage downsample fasta fastq genome-analysis random rust subsampling

Keywords from Contributors

transformers sequence package-management measur archiving compose animals optimize generic conversion

Last synced: 3 months ago
JSON representation

Acceptance Criteria

Revelant topics? true
External users? true
Open source license? true
Active? true
Fork? false

Repository metadata

Randomly subsample sequencing reads or alignments

Host: GitHub
URL: https://github.com/mbhall88/rasusa
Owner: mbhall88
License: mit
Created: 2019-09-26T13:25:47.000Z (over 6 years ago)
Default Branch: main
Last Pushed: 2025-10-21T00:35:00.000Z (3 months ago)
Last Synced: 2025-10-21T01:29:18.824Z (3 months ago)
Topics: alignment, bam, bioinformatics, coverage, downsample, fasta, fastq, genome-analysis, random, rust, subsampling
Language: Rust
Homepage: https://doi.org/10.21105/joss.03941
Size: 13.4 MB
Stars: 244
Watchers: 4
Forks: 20
Open Issues: 3
Releases: 0
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE

Owner metadata

Name: Michael Hall
Login: mbhall88
Email:
Kind: user
Description: Postdoc @ University of Queensland with @LeahRoberts Bioinformatics | Nanopore | Microbial Genomics | Software Dev.
Website: https://mbh.sh
Location: Sunshine Coast, Australia
Twitter:
Company: University of Queensland | UQCCR
Icon url: https://avatars.githubusercontent.com/u/20403931?v=4
Repositories: 131
Last ynced at: 2025-10-07T05:02:40.720Z
Profile URL: https://github.com/mbhall88

GitHub Events

Total

Create event: 14
Release event: 3
Issues event: 9
Watch event: 32
Delete event: 7
Issue comment event: 32
Push event: 32
Pull request review event: 5
Pull request review comment event: 2
Pull request event: 41
Fork event: 2

Last Year

Create event: 14
Release event: 3
Issues event: 9
Watch event: 31
Delete event: 7
Issue comment event: 32
Push event: 32
Pull request review event: 5
Pull request review comment event: 2
Pull request event: 41
Fork event: 2

Committers metadata

Last synced: 3 months ago

Total Commits: 273
Total Committers: 7
Avg Commits per committer: 39.0
Development Distribution Score (DDS): 0.245

Commits in past year: 37
Committers in past year: 3
Avg Commits per committer in past year: 12.333
Development Distribution Score (DDS) in past year: 0.432

Name	Email	Commits
Michael Hall	m**l@m**h	206
Michael Hall	m**8@g**m	46
dependabot[bot]	4****]	17
Pierre Marijon	p**t@a**r	1
George Bouras	8****3	1
Andrew Kane	a**w@a**g	1
Pierre Marijon	p**n@h**e	1

Committer domains:

Issue and Pull Request metadata

Last synced: 3 months ago

Total issues: 43
Total pull requests: 65
Average time to close issues: 5 months
Average time to close pull requests: about 8 hours
Total issue authors: 24
Total pull request authors: 5
Average comments per issue: 2.33
Average comments per pull request: 0.35
Merged pull request: 49
Bot issues: 0
Bot pull requests: 32

Past year issues: 5
Past year pull requests: 39
Past year average time to close issues: 10 days
Past year average time to close pull requests: about 9 hours
Past year issue authors: 5
Past year pull request authors: 3
Past year average comments per issue: 1.6
Past year average comments per pull request: 0.31
Past year merged pull request: 23
Past year bot issues: 0
Past year bot pull requests: 30

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/mbhall88/rasusa

Top Issue Authors

mbhall88 (16)
tseemann (3)
natir (2)
npdungca (2)
camilogarciabotero (1)
ilyavs (1)
nbenzakour (1)
amnotagoldfish (1)
k3yavi (1)
nirajmehta96 (1)
MostafaYA (1)
pmielle (1)
AnupamGautam (1)
ankane (1)
genignored (1)

Top Pull Request Authors

dependabot[bot] (32)
mbhall88 (28)
ankane (2)
gbouras13 (2)
natir (1)

Top Issue Labels

enhancement (10)
bug (1)
help wanted (1)

Top Pull Request Labels

dependencies (32)
rust (27)
autorelease: pending (7)
autorelease: tagged (5)
github_actions (3)

Package metadata

Total packages: 1
Total downloads:
- cargo: 18,864 total
Total dependent packages: 0
Total dependent repositories: 0
Total versions: 18
Total maintainers: 1

crates.io: rasusa

Randomly subsample reads or alignments

Homepage: https://github.com/mbhall88/rasusa
Documentation: https://docs.rs/rasusa/
Licenses: non-standard
Latest release: 2.2.2 (published 5 months ago)
Last Synced: 2025-10-26T03:05:19.382Z (3 months ago)
Versions: 18
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 18,864 Total
Rankings:
- Stargazers count: 12.399%
- Forks count: 14.898%
- Average: 24.489%
- Dependent repos count: 29.318%
- Downloads: 32.017%
- Dependent packages count: 33.812%
Maintainers (1)
- mbhall88

Dependencies

Cargo.lock cargo

adler 1.0.2
aho-corasick 0.7.18
anyhow 1.0.58
assert_cmd 0.10.2
atty 0.2.14
autocfg 1.1.0
bgzip 0.2.1
bitflags 1.3.2
buf_redux 0.8.4
bytecount 0.6.3
bzip2 0.4.3
bzip2-sys 0.1.11+1.0.8
cc 1.0.73
cfg-if 1.0.0
chrono 0.4.19
clap 3.2.8
clap_derive 3.2.7
clap_lex 0.2.4
colored 1.9.3
crc32fast 1.3.2
difference 2.0.0
escargot 0.3.1
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fern 0.5.9
flate2 1.0.24
float-cmp 0.8.0
getrandom 0.1.16
hashbrown 0.12.1
heck 0.4.0
hermit-abi 0.1.19
indexmap 1.9.1
instant 0.1.12
itoa 1.0.2
jobserver 0.1.24
lazy_static 1.4.0
libc 0.2.126
log 0.4.17
lzma-sys 0.1.19
memchr 2.5.0
miniz_oxide 0.5.3
needletail 0.4.1
niffler 2.4.0
normalize-line-endings 0.3.0
num-integer 0.1.45
num-traits 0.2.15
once_cell 1.12.1
os_str_bytes 6.1.0
pkg-config 0.3.25
ppv-lite86 0.2.16
predicates 1.0.8
predicates-core 1.0.3
predicates-tree 1.0.5
proc-macro-error 1.0.4
proc-macro-error-attr 1.0.4
proc-macro2 1.0.40
quote 1.0.20
rand 0.7.3
rand_chacha 0.2.2
rand_core 0.5.1
rand_hc 0.2.0
rand_pcg 0.2.1
redox_syscall 0.2.13
regex 1.5.6
regex-syntax 0.6.26
remove_dir_all 0.5.3
ryu 1.0.10
safemem 0.3.3
serde 1.0.138
serde_derive 1.0.138
serde_json 1.0.82
strsim 0.10.0
syn 1.0.98
tempfile 3.3.0
termcolor 1.1.3
termtree 0.2.4
textwrap 0.15.0
thiserror 1.0.31
thiserror-impl 1.0.31
time 0.1.44
unicode-ident 1.0.1
version_check 0.9.4
wasi 0.9.0+wasi-snapshot-preview1
wasi 0.10.0+wasi-snapshot-preview1
winapi 0.3.9
winapi-i686-pc-windows-gnu 0.4.0
winapi-util 0.1.5
winapi-x86_64-pc-windows-gnu 0.4.0
xz2 0.1.7
zstd 0.7.0+zstd.1.4.9
zstd-safe 3.1.0+zstd.1.4.9
zstd-sys 1.5.0+zstd.1.4.9

Cargo.toml cargo

assert_cmd 0.10 development
predicates 1 development
tempfile 3.1.0 development
anyhow 1.0
chrono 0.4
clap 3.2.8
fern 0.5
log 0.4
needletail 0.4.1
niffler 2.3
rand 0.7.2
rand_pcg 0.2.1
regex 1.5.5
thiserror 1.0

.github/workflows/release.yaml actions

actions-rs/cargo v1 composite
actions-rs/toolchain v1 composite
actions/checkout v2 composite
actions/upload-artifact master composite
softprops/action-gh-release 59c3b4891632ff9a897f99a91d7bc557467a3a22 composite

.github/workflows/rust-ci.yaml actions

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actions-rs/tarpaulin v0.1 composite
actions-rs/toolchain v1 composite
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Dockerfile docker

bash 5.1 build
rust 1.62 build

Score: 17.3003621180817

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