v0.6.1

2024-04-09

• Made -u estimation with short-reads slightly more robust. See CHANGELOG.
• v0.6.0 has a conda install issue. Hopefully v0.6.1 fixes...

latest

Commits

• d0d44f9: Update README.md (Jim Shaw)
• 62a32f1: Update README.md (Jim Shaw)
• ca28402: Update README.md (Jim Shaw)
• f57e486: Update README.md (Jim Shaw)
• 8158e6c: v0.6.1 initial - refactored some code and added automatic diversity detection for estimating identity (bluenote-1577)
• 5db2d41: Update README.md (Jim Shaw)
• 14d3580: Update README.md (Jim Shaw)
• cc39ba4: Update README.md (Jim Shaw)
• a931df9: Update README.md (Jim Shaw)
• 83409c2: Update README.md (Jim Shaw)
• 02232c7: v0.6.1 fixed bug with -I. pushing now to try and fix conda... (bluenote-1577)
• 41a4a50: Merge branch 'main' of https://github.com/bluenote-1577/sylph (bluenote-1577)
• 2c75d89: README (bluenote-1577)

v0.6.0

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 ...

v0.5.1

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.

v0.5.0

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)

v0.4.1

sylph v0.4.1 - getting ready for preprinting

MINOR

• A few minor changes to help texts and options. Also fixed versioning issue.

v0.4.0

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.

v0.3.0

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

v0.2.0

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

v0.1.0

First major release of sylph. See CHANGELOG.md for information.