Hi @bluenote-1577,

-o option seems to be ignored while sketching samples.

Could you fix this?

Hi @bluenote-1577,

I installed sylph using bioconda but it crashed immediately with the following error "Illegal instruction (core dumped)".
Notably, the executable available on github works.

Best,
Florian

I have tested using a 20M 50-bp sequencing fastq for pathogen identification, but I didn't get any results.
Is this software only suitable for applications with large data volumes such as gut microbiota?

Hi @bluenote-1577,

Maybe it's on purpose, but the debug and trace option do not generate a different output.
Yet, I am interested by some statistics such as the number of deduplicated reads.

Hi, I want to use sylph to taxonomically profile a set of contigs against the GTDB v220 database. I installed sylph v.0.6.1 with conda.

I sketched the database from the contigs like this:
sylph sketch contigs.fa -i -o contigs

then I want to do the taxonomic profiling like this:
sylph profile contigs.syldb v0.3-c200-gtdb-r214.syldb -o contigs_gtdb_sylph_results.tsv

But I get the error:
2024-06-28T12:45:16.610Z INFO [sylph::contain] Obtaining sketches...
2024-06-28T12:45:16.610Z ERROR [sylph::contain] No read files found; see sylph query/profile -h for help. Exiting

Apparently sylph is looking for read files, and doesn't understand it's a contig database. Could you help me fix this problem?

Thanks a lot in advance

Hello! Working on getting a Docker image built over in StaPH-B/docker-builds#816 and noticed this during compilation:

#10 50.29    Compiling sylph v0.4.1 (/sylph-0.4.1)
#10 50.84 warning: call to `.clone()` on a reference in this situation does nothing
#10 50.84    --> src/contain.rs:485:47
#10 50.84     |
#10 50.84 485 |         let file = File::open(read_sketch_file.clone()).expect(&format!(
#10 50.84     |                                               ^^^^^^^^ help: remove this redundant call
#10 50.84     |
#10 50.84     = note: the type `str` does not implement `Clone`, so calling `clone` on `&str` copies the reference, which does not do anything and can be removed
#10 50.84     = note: `#[warn(noop_method_call)]` on by default

Is this something we need to be concerned with? cc @erinyoung

Hello

Does sylph works with long nanopore reads ?

Best

Hello, thanks for this amazing tool!

Just wanted to confirm which version of the IMG/VR4 database you made the pre-sketched viral database from.
And whether you possess the corresponding metadata file.

Thank you!

Hi @bluenote-1577,

I have downloaded Illumina sequencing data of the ZymoBIOMICS Fecal Reference.
Then, I have performed taxonomic profiling with sylph (database: gtdb_r207, parameters: --estimate-unknown --read-length 150)
and with meteor, the tool we are currently developping based on species specific marker genes.

Then, I have compared species coverage of both tool in this log-scale scatterplot:

As you can see, both tools have good agreement for high coverage (lambda) species but sylph starts overestimating coverage when it reestimates lambda with its statistical model.
In addition, syplh fails to detect species below ~ 0.2x coverage which is one order of magnitude above the detection limit with simulated data.

There are strain mixtures of the same species in this sample that may explain this strange behaviour.

Your feedback is welcomed,
Florian

Feature requests

Purpose: this is a place to easily log suggestions/feature requests. E.g:

• "I want to display XXX output as an option!"
• "I want to be able to combine database sketches!"

Give a rationale and provide concise/clear instructions if possible. Opinions are welcome too.

You're welcome to email me or open another issue. This thread is to aggregate suggestions without the hassle of opening another issue.

Current feature requests

Here are some current feature requests.

Originally posted by @jolespin in bluenote-1577/skani#23 (comment)

• Option for renaming samples. Sylph currently fixes each sample sketch to the read names. ` done in v0.5.0
• Command line options for inspecting database sketches.
• Command line option to append/merge databases.
• Line-delimited file for database sketches for sylph profile/query done in v0.5.0

@fplaza #6 (comment)

• Save read length while sketching so the user does not have to provide it to compute true coverage. done in v0.5.0

#7

• Different ways of sketching reads and groupings

Hi -

I'm interested in obtaining estimates of relative abundance across all domains of life. Is this possible with sylph? If so, it's unclear to me if that would entail concatenation of pre-built databases or whether a simple merge (after sylph_to_taxprof.py) would be sufficient.

Thanks very much.

Hello,
Please I would like to know if I can create my own database with fungi included.
Also, I am using RefSeq224 data files which are *.fna.gz will the command pick that instead of the fa.gz in your example?
Thanks

Can sylph profile ITS dataset? I downloaded the UNITE fasta file and converted it to the syldb. Then, I tested this tool with some ITS dataset and didnt get any luck to get some outputs. Thanks

Hi,

I've been trying to run the sylph sketch command on a forward and reverse short read set using command:

sylph sketch -1 4914_4_cat_R*

The reads files are in form of:

4914_4_cat_R1.fastq.gz 4914_4_cat_R2.fastq.gz

The command fails with output:

2024-05-08T18:01:26.964Z ERROR [sylph::sketch] Different number of paired sequences. Exiting.

I double checked the short read sets, and the number of sequences in the R1 and R2 fastq files are the same - 4,078,148 as confirmed by both seqkit stats and manual awk screening of the read files.

Any clue on what I could do here would be appreciated.

Thank you!