LotuS rRNA pipeline

Contact owners and managers

1–30 of 32

Welcome to the LotuS webhelp group.

I'll try to answer questions and bug reports as soon as possible, but sometimes some delay is inevitable.

Please only post LotuS related questions, pipeline recipes and options for specific settings and bug reports.

0 selected

Kombucha UGent

5/10/24

Import data

Dear dr. Hildebrand, I have some trouble importing my data in the galaxy server and running the

unread,

Import data

Dear dr. Hildebrand, I have some trouble importing my data in the galaxy server and running the

5/10/24

Justin Stewart, Falk Hildebrand3

3/7/24

Lotus2 does not read -taxAligner

Thanks! this helped! On Tuesday, August 1, 2023 at 3:31:19 PM UTC+2 Falk Hildebrand wrote: Hey Justin

unread,

Lotus2 does not read -taxAligner

Thanks! this helped! On Tuesday, August 1, 2023 at 3:31:19 PM UTC+2 Falk Hildebrand wrote: Hey Justin

3/7/24

Rahul Jain, Falk Hildebrand2

8/1/23

Using lotus2 for Nanopore amplicon seq data

Dear Raahul, please see the github for lotus2 questions: Issues · hildebra/lotus2 (github.com) ( this

unread,

Using lotus2 for Nanopore amplicon seq data

Dear Raahul, please see the github for lotus2 questions: Issues · hildebra/lotus2 (github.com) ( this

8/1/23

Zihao Zhao, Falk Hildebrand2

8/1/23

Segmentation fault

Hey Zihao, apologies, I check this group only rarely these days (please use github if possible). 334

unread,

Segmentation fault

Hey Zihao, apologies, I check this group only rarely these days (please use github if possible). 334

8/1/23

Stephane Plaisance, Falk Hildebrand3

2/15/22

correct pacbio command

I think I might have deleted a message here as it needed approval. If I remember correctly it was

unread,

correct pacbio command

I think I might have deleted a message here as it needed approval. If I remember correctly it was

2/15/22

Stephane Plaisance, Falk Hildebrand2

2/14/22

combining paired-read and long-read analyses

Hey, There is no sensible way I see to combine these results.. the clustering would be influenced by

unread,

combining paired-read and long-read analyses

Hey, There is no sensible way I see to combine these results.. the clustering would be influenced by

2/14/22

sabrina.ber...@gmail.com, Falk Hildebrand4

6/2/20

Q&A

pb "undecided fastq version" with hiseq4000 data

Hey, mhm just looking at the wiki fast page, hiseq 4000 should be the ill 1.8+ protocol and your qual

unread,

Q&A

pb "undecided fastq version" with hiseq4000 data

Hey, mhm just looking at the wiki fast page, hiseq 4000 should be the ill 1.8+ protocol and your qual

6/2/20

fule...@gmail.com

2/10/20

Q&A

uparse question

Dear Falk, I am dealing with an ITS dataset (earth microbiome amplification protocol) and I have

unread,

Q&A

uparse question

Dear Falk, I am dealing with an ITS dataset (earth microbiome amplification protocol) and I have

2/10/20

ullo...@googlemail.com2

12/17/19

Q&A

SILVA SSU 138

yes they are :) https://ftp.arb-silva.de/release_138/Exports/

unread,

Q&A

SILVA SSU 138

yes they are :) https://ftp.arb-silva.de/release_138/Exports/

12/17/19

linda....@gmail.com, Falk Hildebrand2

11/13/19

Q&A

temporary files removed

Hey Linda, sorry for the late reply. The temp files are only for debugging purposes from my

unread,

Q&A

temporary files removed

Hey Linda, sorry for the late reply. The temp files are only for debugging purposes from my

11/13/19

sonumu...@gmail.com, Falk Hildebrand2

11/13/19

Q&A

SDM demultiplexing issue for paired end fastq file

Hey Sunil, there is no second fastq file given, the sdm syntax is actually different. Eg "-

unread,

Q&A

SDM demultiplexing issue for paired end fastq file

Hey Sunil, there is no second fastq file given, the sdm syntax is actually different. Eg "-

11/13/19

Falk Hildebrand

3/27/18

Q&A

Re: Demultiplex reads with multiple primers and barcodes

Hey Kristjan, you need to run LotuS twice, once for each 16S primer. Later the matrices can be

unread,

Q&A

Re: Demultiplex reads with multiple primers and barcodes

Hey Kristjan, you need to run LotuS twice, once for each 16S primer. Later the matrices can be

3/27/18

amin...@hotmail.com, Falk Hildebrand9

9/7/17

Q&A

Failed sdm demultiplexing step: What is the problem?

Hey, -sample_sep is an internal command, please don't modify it. Please send your mapping file to

unread,

Q&A

Failed sdm demultiplexing step: What is the problem?

Hey, -sample_sep is an internal command, please don't modify it. Please send your mapping file to

9/7/17

Bindu Naik, Falk Hildebrand4

7/25/17

Q&A

single reads

Hey Bindu, sorry for the late answer, I was travelling the last 3 weeks. the header might be the

unread,

Q&A

single reads

Hey Bindu, sorry for the late answer, I was travelling the last 3 weeks. the header might be the

7/25/17

qinglong wu, Falk Hildebrand5

5/30/17

Q&A

Found double ID 3 (Extending OTU Seeds step)

Thanks, Falk! Yes, as you expected, I found the repeated header name in derep.hq.fq file. That means

unread,

Q&A

Found double ID 3 (Extending OTU Seeds step)

Thanks, Falk! Yes, as you expected, I found the repeated header name in derep.hq.fq file. That means

5/30/17

jobl...@gmail.com, Falk Hildebrand2

5/15/17

Q&A

Q+A about dereplication and clustering-seed extension

Thanks Jolien for posting the email, as I though this might interest more users! best, Falk

unread,

Q&A

Q+A about dereplication and clustering-seed extension

Thanks Jolien for posting the email, as I though this might interest more users! best, Falk

5/15/17

jobl...@gmail.com, Falk Hildebrand2

5/15/17

Q&A

sdm quality filtering - output files

Hey Jolien, 1) these are only hiQual sequences 2) No, these are filtered. If you are only interested

unread,

Q&A

sdm quality filtering - output files

Hey Jolien, 1) these are only hiQual sequences 2) No, these are filtered. If you are only interested

5/15/17

Luis Morgado, Falk Hildebrand12

5/5/17

Q&A

Parsing paired barcoded reads from Myseq empty reads

Just a quick note on this, the command "sdm -i_fastq <full path to fastq> -map <full

unread,

Q&A

Parsing paired barcoded reads from Myseq empty reads

Just a quick note on this, the command "sdm -i_fastq <full path to fastq> -map <full

5/5/17

jobl...@gmail.com2

4/14/17

Q&A

question about order of analysis events in Lotus + answer

Roughly steps happen in this order: 1-3 is done in sdm 5+4. only high quality, derep passed reads are

unread,

Q&A

question about order of analysis events in Lotus + answer

Roughly steps happen in this order: 1-3 is done in sdm 5+4. only high quality, derep passed reads are

4/14/17

qinglong wu, Falk Hildebrand3

3/10/17

Q&A

Can LotuS pipeline with sdm generate stitched reads in output directory for closed-reference OTU picking in QIIME???

Thanks, Falk! Yes, I will think the closed-reference picking carefully in the future. Much

unread,

Q&A

Can LotuS pipeline with sdm generate stitched reads in output directory for closed-reference OTU picking in QIIME???

Thanks, Falk! Yes, I will think the closed-reference picking carefully in the future. Much

3/10/17

qinglong wu, Falk Hildebrand7

3/10/17

Q&A

LotuS run incomplete in sdm step

Thanks, Falk! Everything is clear to me now. Best, Qinglong

unread,

Q&A

LotuS run incomplete in sdm step

Thanks, Falk! Everything is clear to me now. Best, Qinglong

3/10/17

hao.zh...@gmail.com, Falk Hildebrand2

3/8/17

Q&A

SILVA database cannot access

Hey Hao, sorry for the late answer, but I hope I can still help you. I think there was a time when

unread,

Q&A

SILVA database cannot access

Hey Hao, sorry for the late answer, but I hope I can still help you. I think there was a time when

3/8/17

anke.s...@gmail.com, Falk Hildebrand2

3/8/17

Q&A

heterogeneity spacer in mapping file

Hey Anke, also here sorry for the late answer, I just found these questions by setting up a new group

unread,

Q&A

heterogeneity spacer in mapping file

Hey Anke, also here sorry for the late answer, I just found these questions by setting up a new group

3/8/17

sam....@gmail.com, Falk Hildebrand2

3/8/17

Q&A

Missing Methanomassiliicoccus

Hey Sam, sorry for the late answer, just saw that my email alerts were deactivated for this group. If

unread,

Q&A

Missing Methanomassiliicoccus

Hey Sam, sorry for the late answer, just saw that my email alerts were deactivated for this group. If

3/8/17

Scott Handley, Falk Hildebrand3

5/5/16

Q&A

Problems with sdm on MiSeq 300 kit data

Hi Falk, As always, thanks for the awesome reply and the willingness to adapt. I was wondering if it

unread,

Q&A

Problems with sdm on MiSeq 300 kit data

Hi Falk, As always, thanks for the awesome reply and the willingness to adapt. I was wondering if it

5/5/16

Falk Hildebrand, Jan Söderman5

5/2/16

Q&A

Re: incomplete biom file

Hi Falk, I can now confirm that the latest lotus.pl version does work. I get a biom-file with the

unread,

Q&A

Re: incomplete biom file

Hi Falk, I can now confirm that the latest lotus.pl version does work. I get a biom-file with the

5/2/16

bbroo...@gmail.com, Falk Hildebrand4

4/10/16

Q&A

order of taxonomic assignment, refDF flag

Hey, Thanks, I changed it on the webpage. best, Falk

unread,

Q&A

order of taxonomic assignment, refDF flag

Hey, Thanks, I changed it on the webpage. best, Falk

4/10/16

sam....@gmail.com, Falk Hildebrand10

4/7/16

Q&A

Lost reads in pair 1 after the update to 1.502

Yes, substract the primer length from the previous used length threshholds. But beware that the

unread,

Q&A

Lost reads in pair 1 after the update to 1.502

Yes, substract the primer length from the previous used length threshholds. But beware that the

4/7/16

Scott Handley, Falk Hildebrand6

4/4/16

Q&A

Taxonomic Assignment error with latest version

Great! I also updated the autoinstaller in the new lotus version, and the bug is fixed with the

unread,

Q&A

Taxonomic Assignment error with latest version

Great! I also updated the autoinstaller in the new lotus version, and the bug is fixed with the

4/4/16

handle...@gmail.com, Falk Hildebrand3

3/28/16

Q&A

Can not sync read pairs, while explicit MID sequences are being used! (not supported, sorry)

Many thanks Falk! Everything seems to be working now. I have run several iterations with no problems.

unread,

Q&A

Can not sync read pairs, while explicit MID sequences are being used! (not supported, sorry)

Many thanks Falk! Everything seems to be working now. I have run several iterations with no problems.

3/28/16