# Journal club **URL:** https://forum.mothur.org/c/journal-club/11.md [Latest](https://forum.mothur.org/latest.md) · [Categories](https://forum.mothur.org/categories.md) --- ## [About the Journal club category](https://forum.mothur.org/t/about-the-journal-club-category/19)
**Author:** [@system](https://forum.mothur.org/u/system)\ **Replies:** 0\ **Last updated:** [November 4, 2009, 6:43pm UTC](https://forum.mothur.org/t/about-the-journal-club-category/19 "2009-11-04T18:43:19Z")
Did you see the latest paper in the Journal of My Impact Factor is Better than Yours? --- ## [16S database of medically important bacteria](https://forum.mothur.org/t/16s-database-of-medically-important-bacteria/3480)
**Author:** [@jitendrakeshri](https://forum.mothur.org/u/jitendrakeshri)\ **Replies:** 2\ **Last updated:** [January 15, 2018, 8:08am UTC](https://forum.mothur.org/t/16s-database-of-medically-important-bacteria/3480 "2018-01-15T08:08:31Z")
Hi, I wish to see the curated 16S database for medically important bacteria. In literature, there was one suggestion of 16SpathDB. http://147.8.74.24/16SpathDB/main.php Unforntunately, it is not working now. Can anyo… --- ## [Classification up to species level](https://forum.mothur.org/t/classification-up-to-species-level/3479)
**Author:** [@jitendrakeshri](https://forum.mothur.org/u/jitendrakeshri)\ **Replies:** 2\ **Last updated:** [January 14, 2018, 3:12pm UTC](https://forum.mothur.org/t/classification-up-to-species-level/3479 "2018-01-14T15:12:47Z")
Hi, I wonder if we can classify the 16s rRNA data up to species level. I was going through the EzBioCloud 16S database and there was suggestions that we can classify 16S ngs data up to species level. They have curated f… --- ## [Dealing with samples with low read counts](https://forum.mothur.org/t/dealing-with-samples-with-low-read-counts/3027)
**Author:** [@Dr\_Nezar](https://forum.mothur.org/u/Dr_Nezar)\ **Replies:** 1\ **Last updated:** [November 1, 2016, 5:55pm UTC](https://forum.mothur.org/t/dealing-with-samples-with-low-read-counts/3027 "2016-11-01T17:55:21Z")
Hi, What is the best approach to deal with samples that end up, after removal of chimeras and irrelevant lineages, with low read counts. See the following set for example: Sampleid final read count C1 2517 C2 1781… --- ## [Presenting Metagenomic NGS results in an article with too many species?](https://forum.mothur.org/t/presenting-metagenomic-ngs-results-in-an-article-with-too-many-species/2991)
**Author:** [@mhmtgenc](https://forum.mothur.org/u/mhmtgenc)\ **Replies:** 2\ **Last updated:** [October 20, 2016, 1:29pm UTC](https://forum.mothur.org/t/presenting-metagenomic-ngs-results-in-an-article-with-too-many-species/2991 "2016-10-20T13:29:46Z")
Hi my fellows, I Have analyzed metagenomic NGS data and now I have too many bacteria species and most of them has very low percentage like 0.01 and less values. Since I try to write an article and do some pis charts I c… --- ## [Considerations For Optimizing Microbiome Analysis Using a Marker Gene](https://forum.mothur.org/t/considerations-for-optimizing-microbiome-analysis-using-a-marker-gene/2932)
**Author:** [@jacodela](https://forum.mothur.org/u/jacodela)\ **Replies:** 0\ **Last updated:** [July 26, 2016, 4:48pm UTC](https://forum.mothur.org/t/considerations-for-optimizing-microbiome-analysis-using-a-marker-gene/2932 "2016-07-26T16:48:45Z")
Hi mothur friends, we’ve just published a review that covers one critical aspect that has been overlooked by many researchers, namely, how to properly analyze 16S rRNA microbial data obtained through next-generation seq… --- ## [UPARSE pipeline](https://forum.mothur.org/t/uparse-pipeline/1481)
**Author:** [@dwaite](https://forum.mothur.org/u/dwaite)\ **Replies:** 14\ **Last updated:** [June 3, 2016, 2:55pm UTC](https://forum.mothur.org/t/uparse-pipeline/1481 "2016-06-03T14:55:05Z")
In case anyone missed it, Robert Edgar has pooled his various usearch programs together into one solid pipeline. I’m in the middle of running some test data through it to see how it compares - the mothur 454 SOP vs. the … --- ## [v4 and the new phyla (Hug/Banfield et.al)](https://forum.mothur.org/t/v4-and-the-new-phyla-hug-banfield-et-al/2812)
**Author:** [@Kendra](https://forum.mothur.org/u/Kendra)\ **Replies:** 2\ **Last updated:** [April 19, 2016, 2:49pm UTC](https://forum.mothur.org/t/v4-and-the-new-phyla-hug-banfield-et-al/2812 "2016-04-19T14:49:39Z")
I haven’t seen any mention of someone looking through the sequences from http://www.nature.com/articles/nmicrobiol201648 or http://www.nature.com/nature/journal/v523/n7559/full/nature14486.html to see how well the v4 pri… --- ## [Impact of training sets on classification of high-throughput](https://forum.mothur.org/t/impact-of-training-sets-on-classification-of-high-throughput/627)
**Author:** [@Shaunson26](https://forum.mothur.org/u/Shaunson26)\ **Replies:** 5\ **Last updated:** [August 14, 2015, 12:06pm UTC](https://forum.mothur.org/t/impact-of-training-sets-on-classification-of-high-throughput/627 "2015-08-14T12:06:35Z")
Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys Jeffrey J Werner, Omry Koren, Philip Hugenholtz, Todd Z DeSantis, William A Walters J Gregory Caporaso, Largus T Angenent, Rob… --- ## [Schirmer et al. MiSeq paper](https://forum.mothur.org/t/schirmer-et-al-miseq-paper/2438)
**Author:** [@JamesoK](https://forum.mothur.org/u/JamesoK)\ **Replies:** 0\ **Last updated:** [July 3, 2015, 2:54pm UTC](https://forum.mothur.org/t/schirmer-et-al-miseq-paper/2438 "2015-07-03T14:54:02Z")
This paper is interesting and has tested various approaches to error-correction for MiSeq 16S data: http://nar.oxfordjournals.org/content/early/2015/01/13/nar.gku1341.full I wondered if there were any plans to implemen… --- ## [Swarm: new amplicon sequence clustering software](https://forum.mothur.org/t/swarm-new-amplicon-sequence-clustering-software/1862)
**Author:** [@adamc83](https://forum.mothur.org/u/adamc83)\ **Replies:** 5\ **Last updated:** [June 10, 2015, 12:45pm UTC](https://forum.mothur.org/t/swarm-new-amplicon-sequence-clustering-software/1862 "2015-06-10T12:45:45Z")
Came across this paper earlier today for a new amplicon sequence clustering software: Paper: https://peerj.com/preprints/386/ Software: https://github.com/torognes/swarm Seems like an interesting, slightly different a… --- ## [My Own](https://forum.mothur.org/t/my-own/2325)
**Author:** [@AliRaza08](https://forum.mothur.org/u/AliRaza08)\ **Replies:** 1\ **Last updated:** [March 30, 2015, 1:54pm UTC](https://forum.mothur.org/t/my-own/2325 "2015-03-30T13:54:24Z")
It seems the average neighbor algorithm is usually gaining inside favor In the same way your own preferred algorithm regarding clustering. can a person suggest a good reference That demonstrates It… --- ## [Dual indexing for 16S microbiomics](https://forum.mothur.org/t/dual-indexing-for-16s-microbiomics/2291)
**Author:** [@brindha\_lekshmisaran](https://forum.mothur.org/u/brindha_lekshmisaran)\ **Replies:** 3\ **Last updated:** [March 20, 2015, 12:41pm UTC](https://forum.mothur.org/t/dual-indexing-for-16s-microbiomics/2291 "2015-03-20T12:41:36Z")
Hi, I wonder if you recommend using the dual indexing approach (Kozich etal 2013) for 16S microbiomics. I was unsure if this method is recommended just for metagenomics. In our lab we do 16S microbiomics of V4 region … --- ## [Robustness and Reproducibility in the Demarcation of OTUs](https://forum.mothur.org/t/robustness-and-reproducibility-in-the-demarcation-of-otus/2000)
**Author:** [@Sebastian](https://forum.mothur.org/u/Sebastian)\ **Replies:** 2\ **Last updated:** [February 11, 2015, 2:14pm UTC](https://forum.mothur.org/t/robustness-and-reproducibility-in-the-demarcation-of-otus/2000 "2015-02-11T14:14:41Z")
Dear mothur community, I’d like to (again) shamelessly advertise a paper that has just been published online, and which may be of some interest to some of you: Schmidt TSB, Matias Rodrigues JF, von Mering C (2014). Lim… --- ## [Running Mothur on supercomputers](https://forum.mothur.org/t/running-mothur-on-supercomputers/2066)
**Author:** [@ifuleyoula](https://forum.mothur.org/u/ifuleyoula)\ **Replies:** 0\ **Last updated:** [October 8, 2014, 8:58pm UTC](https://forum.mothur.org/t/running-mothur-on-supercomputers/2066 "2014-10-08T20:58:38Z")
In case anyone here would be interested, we did some instrumentation on Mothur with OpenMP and saw orders of magnitude speed-up on cluter command and others. Here is the link to the proceeding paper: http://dl.acm.org/ci… --- ## [Kozich et al. 2013 VS Fadrosh et al. 2014](https://forum.mothur.org/t/kozich-et-al-2013-vs-fadrosh-et-al-2014/1882)
**Author:** [@ZH22](https://forum.mothur.org/u/ZH22)\ **Replies:** 1\ **Last updated:** [June 13, 2014, 5:26pm UTC](https://forum.mothur.org/t/kozich-et-al-2013-vs-fadrosh-et-al-2014/1882 "2014-06-13T17:26:06Z")
Hey, I am quite curious to know your thoughts on the Fadrosh paper. I know that Illumina also have a standard method of doing V3-4, although many sources suggest it would be better to stick with V4 or any other where yo… --- ## [Fadrosh et al. heterogeneity spacer](https://forum.mothur.org/t/fadrosh-et-al-heterogeneity-spacer/1860)
**Author:** [@Till](https://forum.mothur.org/u/Till)\ **Replies:** 1\ **Last updated:** [May 21, 2014, 2:32pm UTC](https://forum.mothur.org/t/fadrosh-et-al-heterogeneity-spacer/1860 "2014-05-21T14:32:25Z")
Hi all! Did anyone try that method yet? I’m a little confused by the paper, the main advantage of that variable length primer seems to be a reduction of PhiX spike in. However in the Kozich et al. paper you guys use les… --- ## [OTUs & Ecological Consistency](https://forum.mothur.org/t/otus-ecological-consistency/1815)
**Author:** [@Sebastian](https://forum.mothur.org/u/Sebastian)\ **Replies:** 2\ **Last updated:** [May 2, 2014, 1:12pm UTC](https://forum.mothur.org/t/otus-ecological-consistency/1815 "2014-05-02T13:12:45Z")
Dear mothur community, I’d like to shamelessly advertise a paper we just published that may be interesting to some of you (for the others, sorry for the SPAM :wink: ): Schmidt TSB, Matias Rodrigues JF, Mering von C (2… --- ## [RDP, SILVA, GreenGenes](https://forum.mothur.org/t/rdp-silva-greengenes/1388)
**Author:** [@Rich](https://forum.mothur.org/u/Rich)\ **Replies:** 5\ **Last updated:** [October 1, 2013, 10:06am UTC](https://forum.mothur.org/t/rdp-silva-greengenes/1388 "2013-10-01T10:06:00Z")
Hello Mothur, I wanted to know which classification is better RDP, SILVA, GreenGenes and why. Can we use ARB-silva file directly for classification or only mothur modified files for classification should be used. Thank… --- ## [Your count file does not include the sequence...](https://forum.mothur.org/t/your-count-file-does-not-include-the-sequence/1498)
**Author:** [@dlearman](https://forum.mothur.org/u/dlearman)\ **Replies:** 0\ **Last updated:** [September 11, 2013, 2:22pm UTC](https://forum.mothur.org/t/your-count-file-does-not-include-the-sequence/1498 "2013-09-11T14:22:54Z")
Hello, I am in the process of analyzing some MiSeq 250PE data (16S, 515F/806R). I have been been through the SOP and I am now running one of my samples. At the mothur \> screen.seqs step, I have gotten an error regardi… --- ## [PLOS One paper on mouse colon tissue-associated microbiota](https://forum.mothur.org/t/plos-one-paper-on-mouse-colon-tissue-associated-microbiota/767)
**Author:** [@nickholway](https://forum.mothur.org/u/nickholway)\ **Replies:** 0\ **Last updated:** [January 18, 2012, 7:41am UTC](https://forum.mothur.org/t/plos-one-paper-on-mouse-colon-tissue-associated-microbiota/767 "2012-01-18T07:41:38Z")
Host Genetics and Environmental Factors Regulate Ecological Succession of the Mouse Colon Tissue-Associated Microbiota. Much of the bioinformatics was performed using Mothur. --- ## [Citation for Avg Neighbor as preferred clustering algorithm?](https://forum.mothur.org/t/citation-for-avg-neighbor-as-preferred-clustering-algorithm/609)
**Author:** [@mbakker](https://forum.mothur.org/u/mbakker)\ **Replies:** 1\ **Last updated:** [July 19, 2011, 12:24pm UTC](https://forum.mothur.org/t/citation-for-avg-neighbor-as-preferred-clustering-algorithm/609 "2011-07-19T12:24:00Z")
It seems that the average neighbor algorithm is gaining in favor as the preferred algorithm for clustering. Can anyone suggest a reference that demonstrates that it offers better performance than the other methods (furth… --- ## [UniFrac](https://forum.mothur.org/t/unifrac/338)
**Author:** [@jsahl](https://forum.mothur.org/u/jsahl)\ **Replies:** 1\ **Last updated:** [September 10, 2010, 11:12am UTC](https://forum.mothur.org/t/unifrac/338 "2010-09-10T11:12:22Z")
This out today: http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej2010133a.html Jason --- ## [Chimeric sequence vs. recombination breakpoint?](https://forum.mothur.org/t/chimeric-sequence-vs-recombination-breakpoint/184)
**Author:** [@mbakker](https://forum.mothur.org/u/mbakker)\ **Replies:** 1\ **Last updated:** [April 1, 2010, 2:58pm UTC](https://forum.mothur.org/t/chimeric-sequence-vs-recombination-breakpoint/184 "2010-04-01T14:58:56Z")
I just came across this algorithm for detecting recombination breakpoints, and it has got me wondering whether some of the sequences we flag as chimeric might simply include a recombination breakpoint. Thoughts, anyone? … --- ## [PyroNoise](https://forum.mothur.org/t/pyronoise/140)
**Author:** [@mbakker](https://forum.mothur.org/u/mbakker)\ **Replies:** 3\ **Last updated:** [February 11, 2010, 3:47am UTC](https://forum.mothur.org/t/pyronoise/140 "2010-02-11T03:47:36Z")
Pat Schloss mentioned PyroNoise in the “Announcements” section, and I thought I would start a thread here. The reference is: Quince et al. Nature Methods 6, 639–641 (1 September 2009) | doi:10.1038/nmeth.1361 This so… --- ## [Reviews, please](https://forum.mothur.org/t/reviews-please/42)
**Author:** [@jamesafoster](https://forum.mothur.org/u/jamesafoster)\ **Replies:** 0\ **Last updated:** [November 4, 2009, 6:43pm UTC](https://forum.mothur.org/t/reviews-please/42 "2009-11-04T18:43:19Z")
Can anyone recommend some reviews of the various methods used in the “calculators”? I’m looking for a jump-off point to the published literature here.