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CHANGELOG.md

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sylph v0.6.1: improved automatic detection of sequencing error for -u option

Major

  • Improved automatic estimation of sequencing error for estimating unknown abundances/coverages.

Explanation:

The -u option estimates the % of sequences that are "unknown" i.e. not captured by the database and the "true" coverage. This requires knowledge of sequencing error. Previous versions failed when the sample was too diverse compared to sequencing depth (e.g. low-throughput sequencing or complex (ocean/soil) metagenomes).

New fallback added: For short-reads only, if the diversity is too high relative to sequencing depth, (avg k-mer depth < 3) then 99.5% is used as a fallback sequence identity estimate.

sylph v0.6.0 release: New output column, lazy raw paired fastq profiling: 2024-04-06

Major

  • A new column called kmers_reassigned is now in the profile output. This states how many k-mers are lost due to reassignment for that particular genome.
  • -1, -2 options are now available for sylph profile. You can now do sylph profile database.syldb -1 1.fq -2 2.fq ...

sylph v0.5.1 release: Memory improvement and bug fixes : Dec 27 2023

Major

  • Scalable cuckoo filters are now used for read deduplication for memory savings.
  • Deduplication algorithm improved. v0.5.0 worked poorly on highly (>15%) duplicated read sets.
  • Shorter reads can be sketched now. Down to 32bp instead of 63 bp before.

sylph v0.5.0 release: Big improvements on real illumina data : Dec 23 2023

Major

In previous versions, sylph was underperforming on real illumina data sets. See #5

This is because many real illumina datasets have a non-trivial number of duplicate reads. Duplicate reads mess up sylph's statistical model.

For the single and paired sketching options, a new deduplication routine has been added. This will be described in version 2 of our preprint.

This increases sketching memory by 3-4x but greatly increases performance on real datasets with > 1-2% of duplication, especially for low-abundance genomes.

For paired-end illumina reads with non-trivial (> 1% duplication), sylph can now

  1. detect up to many more species low-abundance species below 0.3x coverage
  2. give better coverage/abundance estimates for low-abundance species

BREAKING

  • sequence sketches (sylsp) have changed formats. Sequences will need to be re-sketched.
  • --read-length option removed and incorporated into the sketches by default. (suggested by @fplaza)

Other changes

  • New warning when -o specified and only reads are sketched (#7)
  • You can now rename sylph samples by specifing a sample naming file with --sample-names or --lS (suggested by @jolespin)
  • Newline delimited files are available in profile and query now (suggested by @jolespin)

sylph v0.4.1 release: getting ready for preprinting

Minor

  • small changes for help text, options, and output texts.

sylph v0.4.0 release: major interface changes

BREAKING

  • renamed sylph contain to sylph query.
  • methods for sketching are drastically different now. E.g. we use -g genome1.fa genom2.fa for specifying genomes and -r read1.fa read2.fq for specifying reads when sketching.

Major

  • -u or --estimate-unknown options are now present for estimating unknown organisms in the sample.
  • When using -u, associated options --read-seq-id and --read-len are available for calculating true coverages with sylph, i.e., coverages concordant with read mapping

Minor

  • Coverage calculation is slightly different now.

sylph v0.3.0 release: first class support for pseudotax, now called "profile" - 2023-10-01

Continuing development of sylph taxonomic profiling.

BREAKING

  • --pseudotax option in previous version is now a new command called profile.
  • Databases are enabled for profiling by default.
  • Changed file suffices to syldb and sylsp.

Major

  • Default parameter changes. --min-spacing is set to 30 now.
  • Made profiling faster with some algorithmic tweaks.
  • Coverage calculated slightly differently
  • Many small software changes with respect to threading and outputs

sylph v0.2.0 release: pseudotax improved - 2023-09-19

BREAKING

  • Sylph's *.sylqueries are no longer compatible with older versions of sylph (< v0.2). Files will need to be resketched.

Major

  • Fixed a major bug for the --pseudotax option that required redesigning file formats. Please use --enable-pseudotax when using using contain --pseudotax from now on.
  • --pseudotax option gives relative abundances now. We are gaining some confidence that this approach gives a rough, but surprisingly decent taxonomic classification.
  • Changed how Eff_cov is calculated. We just use the median coverage now, except when we apply coverage-adjustment

Minor

  • Fixed command line ambiguity for sketching outputs. -s has been replaced with -d for sylph sketch.
  • Sylph outputs the results after processing every sample, instead of batching results, now

sylph v0.1.0 release - 2023-09-03

Major

  • Added --pseudotax option, similar to the -w option in mash screen, where k-mers are assigned to the highest ANI genome so redundancy is removed. The output is a very rough taxonomic classification of the sample.

Minor

  • Some fixes and parameter changes from the v0.0.x releases.