SeqFu toolkit

Mingling sequences in Fasta and Fastq formats ~ Plus other #bioinformatics tips for NGS analyses from the command line

[SeqFu toolkit @SeqFu2]

You can learn more about SeqFu in the website:
Learn more: https://t.co/52qrmbtLV9

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[SeqFu toolkit @SeqFu2]

There is a new and faster way to install the main SeqFu binary:

curl -fsSL "https://t.co/VmpE3qLEgp" | sh

of course, bioconda is still an easy way to get it.

SeqFu is a swiss-army knife for FASTA and FASTQ manipulation and can be a very handy tool for pipelines!

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[SeqFu toolkit @SeqFu2]

This is a screenshot from the terminal, and you can easily install SeqFu from conda with:

```
conda install -c bioconda \
"seqfu>1.28"
```

[SeqFu toolkit @SeqFu2]

Would you like to inspect FASTQ files from your terminal?

`seqfu less` can do that! You can scroll, search for motives and see intuitive colored bars representing quality values.

Check it out here: https://t.co/Bx5oHdkCvN [1/2]

[SeqFu toolkit @SeqFu2]

SeqFu has a new website!
We tried to make it nicer, but also introduced new in-browser applets.

Try these two:
- 📊 STATS to calculate N50, plots, and more for one or more files
- 🔍 LESS to have a small preview of FASTQ files, with oligo match ..

https://t.co/BV08ElFeM9

[SeqFu toolkit @SeqFu2]

@marianattestad Roast me then! There is a major refactoring in the program so this can be very helpful!
https://t.co/KYFRQ9mmif

[SeqFu toolkit @SeqFu2]

SeqFu 1.22.0 is out, with some minor improvements and updates.

It's codenamed #EBAME9 because it features a new `--anvio` mode in "seqfu cat"

https://t.co/YCvrzZqBwB

[SeqFu toolkit @SeqFu2]

What if SeqFu had an #Anvio shortcut?

You could reformat FASTA file 50X faster

[SeqFu toolkit @SeqFu2]

@TrumanLab An example is https://t.co/qxAa1wFCGg (not mandatory but possible).

Check this out too: https://t.co/oQROQslksr preprint with a recommendation are automatically eligible for publishing

[SeqFu toolkit @SeqFu2]

SeqKit 2 is now described in a new paper!
It's great to see this great program growing. Inspiring! https://t.co/xvJerN4Svw

[SeqFu toolkit @SeqFu2]

We got 100 stars, thanks a million!
https://t.co/52qrmbtLV9

[SeqFu toolkit @SeqFu2]

Did you know that fu-index allows you to extract lane and run information from Illumina datasets?

This can be useful when splitying by run (e.g. when running DADA2 or prevent batch effect)

https://t.co/2WZoqjRjr7

[SeqFu toolkit @SeqFu2]

Microsoft wants to buy us, but then they would make `SeqFu (work or school)` and `SeqFu (new)` available through their app store...

[SeqFu toolkit @SeqFu2]

@nomad421 Moved to AlmaLinux https://t.co/VLBhgYI2dR

[SeqFu toolkit @SeqFu2]

@BonfieldJames or `seqfu cat` :)

[Michael 英泉 Eisen @mbeisen]

Complain all you want about peer review @FrontiersIn, but its current manifestation is the logical extension of a toxic, dysfunctional and irrational publishing culture that treats papers as currency and continues to propagate the lie that "peer reviewed" means "valid".

[SeqFu toolkit @SeqFu2]

@blelbach Yes, but...

[SeqFu toolkit @SeqFu2]

🥖 Freshly baked: Fasten by @lskatz was just published in @JOSS_TheOJ.
Of course, it's a fast FASTQ manipulation toolkit, written in Rust.

UNIX pipes provided. Bring your own dataset :)

[Ben WoOdcroft @wwood]

Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs.

We applied it to 250,000 metagenomes- in environmental samples 75% lack a genome/MAG (abundance-weighted). A 🧵https://t.co/c3kfgWEVjh

[SeqFu toolkit @SeqFu2]

@mbeisen yes but did you explain they were emotional support flies?