A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

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And this is what we suggested updating it with:

Hi <@U05LNHCFLCW> great plan. I'm actually stitching together denovotranscript and metatdenovo.

I was just wondering, what are you planing to use as input for transdecoder? is it the fasta after transcriptome merge (CAT directory at the moment)?

I'm sure the figure is a draft and will be updated later,
cheers

Wow! Great to hear that someone is already on it :smile:

<@U08L6AY8DHB> can you give the specifics on the transdecoder input please? ;)

I was also wondering if you would also be interested to incorporate intron seeker for retained introns...

<https://doi.org/10.21105/joss.06272>

Hmm, can't find a bioconda environement, and only found this github repo: <https://github.com/Bios4Biol/intronSeeker>
But it's only HTML code

Oh, there are python scripts in the repo though, so could probably do something, yes

yea, there's a yml file, if interested, I could set a singularity/apptainer for it

bioconda would be the best!! In order to create an nf-core module out of it :wink:

then it automatically loads containers to quay and galaxy, for docker and singularity

Hello <@U08G34SHRFG>!

Thank you for stitching together denovotranscript and metatdenovo!

The idea is to feed the merged transcriptome FASTA file into TransDecoder to detect open reading frames using this command: `TransDecoder.LongOrfs -t target_transcripts.fasta` . I just found that you can implement Pfam hits using this command `hmmscan --cpu 8 --domtblout pfam.domtblout /path/to/Pfam-A.hmm transdecoder_dir/longest_orfs.pep` the Pfam-A.hmm is easily obtained from here: <https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz> and integrate this information into this command `TransDecoder.Predict -t target_transcripts.fasta --retain_pfam_hits pfam.domtblout`  . This will definitely improve the the accuracy of the results.

Also, I support using IntronSeeker for retained intron detection.

Thank you  for this great suggestion!