Category: Bioinformatics

Postdoc with Erik Kristiansson

If you are skilled in bioinformatics and want to work with one of my favorite persons, you should check out this postdoc ad closing January 9. This two-year position in Erik Kristiansson‘s lab at Chalmers University of Technology is a great opportunity to work with fantastic people on highly interesting questions. It has applications in infectious diseases and antibiotic resistance, and will be focused on genomic analysis of antibiotic resistance and virulence and their evolutionary history. The work includes both the development of new data-driven methodologies and the application of existing methodology to new datasets. The position will involve collaborations with researchers from clinical microbiology and the environmental sciences within the Centre for Antibiotic Resistance Research.

Open PhD position

We are hiring a PhD student to work with interactions between the bacteria in human and environmental microbiomes that are important for community stability and resilience to being colonized by unwanted bacteria (including pathogens). The project seeks to unearth which environmental and genetic factors that are important determinants of bacterial invasiveness and community stability. You can read more at our Open Positions page.

We are looking for a candidate with experience with both bioinformatics and experimental microbiology. Previous experience with microbial communities is a plus, but not a must, as is work with human cell lines.

The project is fully funded by a grant from the Swedish Research Council and the position is planned for 4.5 years, with 4 years of research and course work and half a year of teaching.

If you feel that you are the right person for this position, you can apply hereWe look forward to your application! The deadline for applications is October 21.

Published preprint: Mitochondrial rRNA contamination

Last week, a preprint describing a study which I have played a small part in was posted on bioRxiv. This paper (1) uses the Metaxa2 database (2) to tease out how much of an effect mitochondrial rRNA sequences have on studies of bacterial diversity in corals. And it turns out that it matters… a lot. Importantly, by supplementing the taxonomic databases with diverse mitochondrial rRNA sequences from the Metaxa2 database, ~97% of unique unclassified sequences could be resolved as mitochondrial, without increasing the level of misannotation in mock communities. Thus the study not only points to a problem, but also to its solution! You can read it all here.


  1. Sonnet D, Brown T, Bengtsson-Palme J, Padilla-Gamiño J, Zaneveld JR: The Organelle in the Room: Under-annotated Mitochondrial Reads Bias Coral Microbiome Analysis. bioRxiv, 431501 (2021). doi: 10.1101/2021.02.23.431501 [Link]
  2. Bengtsson-Palme J, Hartmann M, Eriksson KM, Pal C, Thorell K, Larsson DGJ, Nilsson RH: Metaxa2: Improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data. Molecular Ecology Resources, 15, 6, 1403–1414 (2015). doi: 10.1111/1755-0998.12399 [Paper link]

Metaxa2 Genome mode fixes

Yes, Saturdays are somewhat weird days for software updates, but if you’re doing weekend work anyway, why wait to push bug fixes to the community? A very minor bug-fix update to Metaxa2 was released today, bringing the software to version 2.2.3.

Two things have changed in this version, both related to the genome mode. 1) We fixed a file reading bug in the ‘genome’ mode of the software. This bug caused the last sequence in an input FASTA file not to be read unless there was a newline after it. Since the ‘genome’ mode is rarely used by most users, we suspect not a lot of users have been affected by this bug.
2) While we were at it, we changed the behavior of the ‘genome’ mode to mirror that of the ‘auto’ mode, as the strict genome mode dropped sequences shorter than 2500 bp. We considered this behavior counter-intuitive to what most users would want, and has now changed the ‘genome’ mode to behave the same as the ‘auto’ mode and not drop short sequences.

No other changes have been made in this version. The update can be found at the Metaxa2 software page.

Minor ITSx update

A new version of ITSx is released today. This minor update contains two minor bug fixes and two small new features.

The first bug was that ITSx returned empty sequences in the FASTA file for no detections for large input files. This has now been fixed.

The second bug fix is a bit more fuzzy and involved some fine-tuning of how large input files are handled in ITSx to stabilise E-value and score cut-offs.

The two new features are:

  1. The possbility to put the temporary directory in a custom location using the --temp option.
  2. ITSx now warns when the input file contains sequences with identical identifiers, which usually leads to sequences being dropped from the input file.

The new update brings ITSx to version 1.1.3. Thanks for the users who have spotted bugs and suggested new features! Happy barcoding everyone!

Published paper: CAFE

We start the new year with a bang, or at least a new paper published. Bioinformatics put our paper (1) describing the software package CAFE online today (although it was accepted late last year). The CAFE package is a combination of Perl and R tools that can analyze data from paired transposon mutant sequencing experiments (2-4), generate fitness coefficients for each gene and condition, and perform appropriate statistical testing on these fitness coefficients. The paper is short, but shows that CAFE performs as good as the best competing tools (5-7) while being superior at controlling for false positives (you’ll have to dig into the supplement to find the data for that though).

Importantly, this is a collaborative effort by basically the entire research group from last spring: me, Haveela, Emil, Anna and our visiting student Adriana. A big thanks to all of you for working on this short but important paper! You can read the full paper here.


  1. Abramova A, Osińska A, Kunche H, Burman E, Bengtsson-Palme J (2021) CAFE: A software suite for analysis of paired-sample transposon insertion sequencing data. Bioinformatics, advance article doi: 10.1093/bioinformatics/btaa1086
  2. Chao,M.C. et al. (2016) The design and analysis of transposon insertion sequencing experiments. Nature reviews Microbiology, 14, 119–128.
  3. van Opijnen,T. and Camilli,A. (2013) Transposon insertion sequencing: a new tool for systems-level analysis of microorganisms. Nature reviews Microbiology, 11, 435–442.
  4. Goodman,A.L. et al. (2011) Identifying microbial fitness determinants by insertion sequencing using genome-wide transposon mutant libraries. Nature Protocols, 6, 1969–1980.
  5. McCoy,K.M. et al. (2017) MAGenTA: a Galaxy implemented tool for complete Tn- Seq analysis and data visualization. Bioinformatics, 33, 2781– 2783.
  6. Zhao,L. et al. (2017) TnseqDiff: identification of conditionally essential genes in transposon sequencing studies. BMC Bioinformatics, 18.
  7. Zomer,A. et al. (2012) ESSENTIALS: Software for Rapid Analysis of High Throughput Transposon Insertion Sequencing Data. PLoS ONE, 7, e43012.

Minor update of Metaxa2

Today, we released a minor update to Metaxa2, bringing it to version 2.2.2. The new version includes some bug fixes related to the Metaxa2 Database Repository, as well as a new “–temp” option allowing the user to specify the location for the temporary files. No other changes have been made in this version.

The update can be found at the Metaxa2 software page.

Metaxa2 update compatible with HMMER 3.3

Exactly two years after we released the Metaxa2 database builder, here’s the first update to the software. Unfortunately, it is just a boring bug fix, but the good part is that brings back compatibility with the new version of HMMER (3.3) released in November 2019 (as noted here). It seems like it is mainly the Database builder which has been impacted with by this incompatibility, but we recommend everyone to update.

We have tried to bug check this version as good as we can to make sure we did not break any features while introducing this new compatibility. We think that this version is bug free, but as we wanted to push this out quickly, please be more observant than usual to odd behaviour, and make sure to report any bugs!

The update can be downloaded here:

Major problem with Metaxa2 and HMMER 3.3

Update: There is now an updated version of Metaxa2 that addresses this problem. Find it here.

We have recently discovered that the new version of HMMER (3.3) released in November 2019 have introduced new restrictions that make it partially incompatible with Metaxa2. The most apparent problem is in the Database Builder software, which will not build profiles properly in most cases. Instead, HMMER will return an error and only some profiles will be created.

We do currently not know if this also affects the functionality of Metaxa2 itself. We are currently investigating this.

For now, the solution to this problem is to use the previous version of HMMER (version 3.2.1) while we investigate further. That version can be downloaded here:

I am sorry about not discovering this earlier, this only came to our attention this week!

Open postdoc position

We are hiring a postdoc to work with environmental monitoring of antimicrobial resistance. The project is part of the EMBARK program and will consider different aspects of establishing a baseline for background antibiotic resistance in the environment, standardization of monitoring protocols and development of methods to detect emerging resistance threats. The project will involve work with environmental sampling, DNA extractions, bacterial culturing and generation of large-scale DNA sequence data. In terms of bioinformatic analyses, the project will encompass analysis of next-generation sequence data, genome-resolved metagenomics, short-read assembly and network analysis.

We look for a skilled bioinformatician, preferably with experience of experimental laboratory work. If you feel that you are the right person for this position, you can apply here. More information is also available here. We look forward to your application! The deadline for applications is January 3.