Unbinned Contigs fasta file?

[Anna-MarieSeelen]

Dear aviary developers,

I was wondering if there is a file in your output that contains all the unbinned contigs from all the binners combined. I couldn’t find one. I did come across the rosella_bin_unbinned.fasta file, which includes unbinned contigs from Rosella, but some of these contigs also appear in other bins. So, this isn’t exactly what I’m looking for.

If there isn’t a file that compiles all unbinned contigs, I don't understand how SingleM generates the unbinned.otu_table found in the diversity directory or is this a built-in feature of SingleM?

Thanks in advance for your help!

Best regards,

Anna

[wwood]

Hi Anna,

SingleM doesnt look for OTUs in an unbinned contigs file. Instead it looks at raw reads, all assembled contigs, and MAGs. Any OTUs in the contigs and reads than aren't in the MAGs are called unbinned.

HTH, ben

-------------- Ben Woodcroft Group leader, Centre for Microbiome Research, QUT

---

From: Anna-Marie Seelen @.> Sent: Thursday, March 27, 2025 10:42:37 PM To: rhysnewell/aviary @.> Cc: Subscribed @.***> Subject: [rhysnewell/aviary] Unbinned Contigs fasta file? (Issue #268)

Dear aviary developers,

I was wondering if there is a file in your output that contains all the unbinned contigs from all the binners combined. I couldn’t find one. I did come across the rosella_bin_unbinned.fasta file, which includes unbinned contigs from Rosella, but some of these contigs also appear in other bins. So, this isn’t exactly what I’m looking for.

If there isn’t a file that compiles all unbinned contigs, I don't understand how SingleM generates the unbinned.otu_table found in the diversity directory or is this a built-in feature of SingleM?

Thanks in advance for your help!

Best regards,

Anna

― Reply to this email directly, view it on GitHubhttps://github.com/rhysnewell/aviary/issues/268, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAADX5DGY3TXITXNPF2ODYD2WPP23AVCNFSM6AAAAABZ44FUGKVHI2DSMVQWIX3LMV43ASLTON2WKOZSHE2TEOBVHE2DCOI. You are receiving this because you are subscribed to this thread.Message ID: @.***>

[Anna-MarieSeelen]Anna-MarieSeelen created an issue (rhysnewell/aviary#268)https://github.com/rhysnewell/aviary/issues/268

Dear aviary developers,

I was wondering if there is a file in your output that contains all the unbinned contigs from all the binners combined. I couldn’t find one. I did come across the rosella_bin_unbinned.fasta file, which includes unbinned contigs from Rosella, but some of these contigs also appear in other bins. So, this isn’t exactly what I’m looking for.

If there isn’t a file that compiles all unbinned contigs, I don't understand how SingleM generates the unbinned.otu_table found in the diversity directory or is this a built-in feature of SingleM?

Thanks in advance for your help!

Best regards,

Anna

― Reply to this email directly, view it on GitHubhttps://github.com/rhysnewell/aviary/issues/268, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAADX5DGY3TXITXNPF2ODYD2WPP23AVCNFSM6AAAAABZ44FUGKVHI2DSMVQWIX3LMV43ASLTON2WKOZSHE2TEOBVHE2DCOI. You are receiving this because you are subscribed to this thread.Message ID: @.***>