mtsv_tools - v2.0.2

Version 2.0.2

Introduces the --tune-max-hits parameter. Having too many seed hits can cause inefficient runtimes by increasing the number of reverse lookups and position searches. While the --max-hits parameter just skips seeds that have a very high number of hits, the --tune-max-hits parameter doubles the seed interval to reduce the total number of seed lookups per read. This may reduce sensitivity for some reads with many seed hits but it does not have a large impact.

Default parameters have been adjusted to better balance speed and accuracy.

- Rust
Published by tfursten almost 4 years ago

mtsv_tools - v2.0.1

Second Major Version:

1. Updated Rust-Bio data structures.
   • This includes a sampled suffix array which reduces the size of the MG-Indices.
   • Indices built with different major versions will not be compatible.
2. New output format.
   • The binning output now reports the alignment edit distance for hits.
   • The collapse command works with this new output and will not be compatible with previous output format
3. New inputs allowed.
   • The binning command now accepts either FASTA or FASTQ format inputs.
   • The queries no longer need to be the same size.
4. Parameter changes
   • To account for different size queries, the binning parameters have been modified.
   • The edit distance is now a proportion (--edit-rate) based on the length of the read.
   • The --seed-gap parameter was renamed --seed-interval to be more consistent with other tools.
   • The minimum seed threshold (--min-seed) is now a percentage of the number of seeds to allow different size reads.

What's Changed

• Dev by @tfursten in https://github.com/FofanovLab/mtsv_tools/pull/1
• build FM-index from ssa references by @tfursten in https://github.com/FofanovLab/mtsv_tools/pull/2
• Dev by @tfursten in https://github.com/FofanovLab/mtsv_tools/pull/3
• Dev by @tfursten in https://github.com/FofanovLab/mtsv_tools/pull/4
• Update tests by @tfursten in https://github.com/FofanovLab/mtsv_tools/pull/5
• update stopwatch by @tfursten in https://github.com/FofanovLab/mtsv_tools/pull/6

Full Changelog: https://github.com/FofanovLab/mtsv_tools/compare/1.0.2...2.0.0

- Rust
Published by tfursten over 4 years ago

mtsv_tools - v2.0.0

Second Major Version:

1. Updated Rust-Bio data structures.
   • This includes a sampled suffix array which reduces the size of the MG-Indices.
   • Indices built with different major versions will not be compatible.
2. New output format.
   • The binning output now reports the alignment edit distance for hits.
   • The collapse command works with this new output and will not be compatible with previous output format
3. New inputs allowed.
   • The binning command now accepts either FASTA or FASTQ format inputs.
   • The queries no longer need to be the same size.
4. Parameter changes
   • To account for different size queries, the binning parameters have been modified.
   • The edit distance is now a proportion (--edit-rate) based on the length of the read.
   • The --seed-gap parameter was renamed --seed-interval to be more consistent with other tools.
   • The minimum seed threshold (--min-seed) is now a percentage of the number of seeds to allow different size reads.

What's Changed

• Dev by @tfursten in https://github.com/FofanovLab/mtsv_tools/pull/1
• build FM-index from ssa references by @tfursten in https://github.com/FofanovLab/mtsv_tools/pull/2
• Dev by @tfursten in https://github.com/FofanovLab/mtsv_tools/pull/3
• Dev by @tfursten in https://github.com/FofanovLab/mtsv_tools/pull/4
• Update tests by @tfursten in https://github.com/FofanovLab/mtsv_tools/pull/5
• update stopwatch by @tfursten in https://github.com/FofanovLab/mtsv_tools/pull/6

Full Changelog: https://github.com/FofanovLab/mtsv_tools/compare/1.0.2...2.0.0

- Rust
Published by tfursten over 4 years ago

mtsv_tools - v1.0.2

- Rust
Published by tfursten over 4 years ago

mtsv_tools - v1.0.2

Bug Fixes

Fixed coalescing_seed_hits function which combines seed hits into candidate regions in index.rs 1. Off by one comparing reference boundary and seedhit boundary. 2. No longer loses previous seed hit when a reference boundary is hit. 3. Final candidate from last seed hit is now checked.

Fixed deprecated code

1. Updated trimright with trimend in vendor/rust-bio/src/io/fasta.rs and vendor/rust-bio/src/io/fastq.rs

- Rust
Published by tfursten about 5 years ago

mtsv_tools - v1.0.1

This release adds an additional maxhits parameter to mtsv-binner which allows the cutoff for seed hits to be modified. Any seed that has over maxhits will be ignored. This was previously hard coded at 100,000 but other seed based aligners allow this to be modified and often have a default much lower than 100,000. The default is now 20,000 which runs much faster while having a small impact on the binning results.

- Rust
Published by tfursten about 6 years ago

mtsv_tools - First Release

First release of core alignment based metagenomic binning tools.

- Rust
Published by tfursten over 6 years ago