This is the home of publicly available software I have written or been involved in. All software distributed through this page is free for non-commercial use and copying (unless otherwise specified in the package itself). For commercial use, please contact me – I won’t be impossible about giving it away for free, but I would like to have some control over what my ideas are used for outside the academia.
- Metaxa – a software package for automated identification and classification of small subunit (SSU) rRNA sequences from archaea, bacteria, eukaryotes, chloroplasts and mitochondria in metagenomic and environmental sequencing data sets.
- Megraft – a software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes.
- ITSx – a software tool for detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for use in environmental sequencing
- PETKit – a set of tools to ease the use of sequences from large-scale sequencing projects, generating paired-end reads.
- metaorf – a very simple gene finder adapted for the fragmentary nature of metagenomic data. There is no advanced probabilistic model involved in this piece of software, it just looks for open reading frames, allowing (as specified by the user) sequences to start and end outside of the nucleotide reads. For more advanced gene finding in metagenomes I recommend using metagene [article], MetaGeneMark [article] or FragGeneScan [article]. If, however, for some reason you would like the simplicity of ATG-to-TGA prediction, metaorf is the choice for you.
Download (version 1.0)
- bloutminer – a script for mining data from BLAST reports. Allows you to specify e.g. an E-value cutoff, a length cutoff and a percent identity cutoff, and extract a list of the hits satisfying these cutoffs. I normally use an E-value cutoff of 10 for my BLAST searches, and then extracts hits with bloutminer, allowing me to change the cutoffs at a later stage without redoing the whole BLAST search. Is also able to “pool” sequences into groups, based on their sequence tags. In addition, it can also output the N number of best matches to a query.
Download (currently at version 0.9.6)
- Scripts collection – Most of the things found here are just small handy perl or shell scripts, but if you would not bother doing the same work as I have already done, feel free to download and use my solutions.
- You may have to right-click the links to download the files.
- After download, move the files to a place where your unix-like system finds executables (like /usr/local/bin). Personally I have added a directory called “bin” in my home folder to my PATH and usually to put scripts and things there.
- When the file is in place, move into that directory and type:
chmod 744 name_of_the_downloaded_file
where “name_of_the_downloaded_file” should be replaced with the name of the downloaded file, e.g. “blastgrep”
- From now on, you should be able to call the script from anywhere in your system, just as a usual Linux/Unix command.
- For most of my scripts and programs, help and instruction for usage can be found by using the -h flag.
Comments, questions, beers, pizzas, cakes, fruit pies, job positions and other types of feedback to my e-mail address:
firstname.lastname [at] microbiology.se (and my name is, as usual, Johan Bengtsson).