bipype stands for BioInformatics-PYthon-PipE.

• fastx-toolkit v0.0.13
• usearch v7.0.959_i86linux32
• FLASH v1.2.7
• bowtie2 v2.2.4
• samtools v0.1.18
• RAPsearch 2.12_64bits
• MetaVelvet v1.2.01
• HUMAnN v0.99
• SARTools v1.2.0
• KRONA 2.0

Bipype accepts three types of input: amplicons, whole genome sequences (WGS) and metatranscriptomic data. Bipype works with both paired-end and single read sequences. For amplicon (prokaryotic or fungal) data, if needed, paired-end reads are merged and sequence reconstruction is performed. Reconstructed 16S or ITS sequences are searched in proper reference databases and hits to related taxonomic units are counted.

For WGS reads three paths are available. In one they will be used for reconstruction of contigs, which will be further used for reference database search (outside of the pipeline). In the second they will be used directly in taxonomic diversity search, in third they will be compared to sequences related to metabolic pathways.

The biodiversity data at taxonomical and functional levels are similar in their tree structure - we provide display of results in a common form of an interactive HTML tree.

bipype is written in Python 2.7. To install it, clone the repository with command git clone https://github.com/bipype/bipype.git

Check bipype -h for details about running bipype