Diversity estimation pipeline for high-throughput sequencing (Illumina) platforms. This pipeline has been used for analysis of foraminiferal and eukaryotic diversity in
- F Lejzerowicz, P Esling, W Majewski, W Szczuciński, J Decelle, C Obadia, PM Arbizu, J Pawlowski, "Ancient DNA complements microfossil record in deep-sea subsurface sediments", Biology Letters, vol.9, no.4, 2013.
- P Esling, F Lejzerowicz, J Pawlowski "High-throughput accuracy for multiplex amplicon sequencing", Nature Methods, in review.
- J Pawlowski, P Esling, F Lejzerowicz, T Cedhagen, T Wilding "Environmental monitoring through protist NGS metabarcoding: assessing the impact of fish farming on benthic foraminifera communities", Molecular Ecology Resources, in review.
This pipeline has been developped in C language for fast processing. In order to use the pipeline on raw (FASTQ) data, prior to the publication and disclosure of its inner methods, we pre-compiled the software for different architectures. Hence, you can find here the executables for the pipeline
- illuminaPipeline-Unix
- illuminaPipeline-MacOS
In all cases, we will refer to these executables as illuminaPipeline in the following.
In order to produce an output of assembly, diversity estimation and statistics, the program should be called in the following manner (in a terminal window)
./illuminaPipeline -forwardFile <Path to R1 FastQ> -reverseFile <Path to R1 FastQ> -taggingFile <Path to list of tags (fasta)> -outputDir <Path to directory for results> -meanQual <Mean read Q (int)> -minBase <Minimum Q of a base> -maxAmb <Maximum number of ambiguous> -primMiss <Number of errors in primer> -tagMiss <Number of errors in tag> -taxonomyFile <Path to taxonomy database (fasta)>
This git-hub repository will also be re-used once the pipeline has been fully disclosed in order to provide the community with the complete source code, so stay in touch.