Nanoq - 0.10.0

New release for read trimming and minor updates :partying_face:

Reads can now be trimmed by a fixed number of bases from the start (--trim-start/-S) and end (--trim-end/-E) [#36]

nanoq -i test.fq -S 100 -E 100 > trim.fq

Read lengths (--read-lengths/-L) and qualities (--read-qualities/-Q) of pass reads can be written to file [#33]

nanoq -i test.fq -Q qual.txt -L len.txt

Other:

• u32 read length values refactored to usize removing max length limitation on x86_64 [#37]
• Filtered read count added to report output (--report/-r) [#34]

Scientific Software - Peer-reviewed - Rust
Published by esteinig almost 3 years ago

Nanoq - 0.9.0

:warning: Breaks compatibility with lower versions :warning:

:warning: Minimum rustc version: 1.56.0 :warning:

• --stats/-s now outputs the summary to stdout [#31]

bash nanoq -i test.fq -s > report.txt

• --report/-r always writes the report to a file

bash nanoq -i test.fq -s -r report.txt nanoq -i test.fq -f -r report.txt > reads.fq

• report output is never output to stderr - use explicit report file when filtering

bash nanoq -i test.fq -r report.txt > reads.fq

• --json/-j always outputs a full report in JSON format [#30]

bash nanoq -i test.fq -j -s > report.json nanoq -i test.fq -j -r report.json > reads.fq

Scientific Software - Peer-reviewed - Rust
Published by esteinig almost 4 years ago

Nanoq - 0.8.6

• added better filter tests [#26] - test coverage 100% :partying_face:
• -H / --header option for machine readable summary output header [#29]

Scientific Software - Peer-reviewed - Rust
Published by esteinig about 4 years ago

Nanoq - 0.8.5

• added --max-qual option to filters
• added minor tests

Scientific Software - Peer-reviewed - Rust
Published by esteinig about 4 years ago

Nanoq - 0.8.4

• update Zenodo data for JOSS
• push synchronized version

Scientific Software - Peer-reviewed - Rust
Published by esteinig about 4 years ago

Nanoq - 0.8.3

JOSS publication:

• https://github.com/openjournals/joss-reviews/issues/2991
• no update to nanoq or release binaries (renamed)
• release and software versions will be harmonized in 0.8.4

Scientific Software - Peer-reviewed - Rust
Published by esteinig over 4 years ago

Nanoq - 0.8.2

• fixed bug in the summary stats output [#24]

Scientific Software - Peer-reviewed - Rust
Published by github-actions[bot] over 4 years ago

Nanoq - 0.8.1

:tada: Nanoq rewrite :tada:

• more rusty code around the needletail parser (rm rust-bio) which provides superior performance
• ultra fast mode (--fast) that ignores quality scores and speeds up read iterations (see benchmarks)
• better explanation of benchmarks for replication, included rust-bio-tools sequence stats
• more minimal implementation of filters and summary reports (rm filtlong analogues)
• better command line interface with structopt
• output compression with niffler
• continuous integration actions
• release binaries
• conda recipe

Scientific Software - Peer-reviewed - Rust
Published by github-actions[bot] over 4 years ago

Nanoq - 0.2.1

0.2.1

• forgot a print statement in --detail :expressionless:
• benchmarks table updated
• minor cosmetic changes

Scientific Software - Peer-reviewed - Rust
Published by esteinig about 5 years ago

Nanoq - 0.2.0

0.2.0

• implements needletail (default) and rust-bio (-c) read parsers
• keep filters cf. filtlong: --keep_bases and --keep_percent
• enhanced output cf. nanostat with --detail flags
• lots of tests: cargo test
• benchmarks Docker container: /paper/Benchmarks
• conda install: conda install -c conda-forge -c esteinig nanoq=0.2.0

Scientific Software - Peer-reviewed - Rust
Published by esteinig about 5 years ago

Nanoq - Zenodo release

Release to archive on Zenodo

Scientific Software - Peer-reviewed - Rust
Published by esteinig almost 6 years ago

Nanoq - 0.1.0

Main functions are working. No tests yet.

IO:

• stream: stdin / stdout no flags or -
• file: --fastq and --output filename

Filters:

• --length minimum read length
• --quality minimum average read quality
• no filters set computes summary stats only

Summary stats to stderr:

• number reads
• base pairs total
• longest read
• shortest read
• mean length
• median length
• mean quality
• median quality

Scientific Software - Peer-reviewed - Rust
Published by esteinig almost 6 years ago