Iorek

This repository contains a collection of programs for analysing sequence data.

• find-motifs finds (short) specified motifs in sequences from a fasta file.
• find-homopolymers finds homopolymer tracts, as well as di- and tri-nucleotide repeats, in sequences from a FASTA file. See the documentation
• translatorator finds sub-sequences of input sequence that match kmers, and translates them into amino acid sequence. See the documentation
• coverotron computes per-base or per-window sequence read coverage from a set of BAM or CRAM files.
• tabulate-alignments reports the count of reads split by read base (or insertion/deletion) and mapping quality at each position in a given range or ranges.
• iorek-qc quantifies the presence of 'true' and 'error' kmers in a set of sequence reads (from a FASTQ file), based on a database of true kmers in jellyfish2 format.
• tabulate-mismatches walks all reads and reports all mismatches / insertions / deletions stratified by their type and flanking sequence. See the documentation
• assess-qualities quantifies the error rate predicted by base qualities, against the observed error rate, in a set of read alignments.
• zoomsa reads a multiple sequence alignment FASTA file, and writes an interactive HTML visualisation of it.

License

Iorek is released under the Boost software license. See the LICENSE.txt file for details.

Iorek makes use of several other libraries that are included in the source repository and released under their own respective licenses. These include:

• boost
• htslib
• SeqLib
• parallel-hashmap
• moodycamel concurrent queue
• jellyfish2
• Eigen
• sqlite3
• zstandard
• catch2
• wfa2

Please see the respective license files in subdirectories of 3rd_party/ for details.

Compilation

iorek is built using the waf build tool, which is bundled with the code. A basic compilation cycle is:

$ ./waf configure
$ ./waf

Executables will appear in build/apps/.

You can also optionally specify an installation prefix and ask waf to install the result:

$ ./waf configure --prefix=[installation path]
$ ./waf install

Executables will be copied to [installation path]/bin/.

Contributors

Iorek was written by Gavin Band with contributions from Tom Roberts.