Sources of programs, scripts, datafiles etc¶

Datafiles¶

Miseq 2 x 150 paired end reads
- originally found at http://www.illumina.com/science/data_library.ilmn, but the data are no longer there. Those interested can find a copy of the subset used in the course here: read1 read2
- random subsampling using seqtk https://github.com/lh3/seqtk
Nextera mate pair reads
- from Illumina basespace https://basespace.illumina.com/‎, look for “Nextera Mate Pair (E. Coli)” https://basespace.illumina.com/project/294296/Nextera-Mate-Pair-E-Coli
PacBio reads
- from https://github.com/PacificBiosciences/DevNet/wiki/E.-coli-Bacterial-Assembly. Subsampling was done using seqtk: seqtk sample m141013_011508_sherri_c100709962550000001823135904221533_s1_p0.filtered_subreads.fastq 0.2 >m141013_011508_filtered_subreads_30x.fastq
MinIOn data
- from Nick Loman, see http://lab.loman.net/2015/09/24/first-sqk-map-006-experiment/. Reads from ENA entry http://www.ebi.ac.uk/ena/data/view/ERR1147227 were downloaded through ftp: ftp://ftp.sra.ebi.ac.uk/vol1/ERA540/ERA540530/oxfordnanopore_native/MAP006-1.tar. 2D reads were extracted using poretools 0.5.1 with poretools fastq --type 2D MAP006-1/MAP006-1_downloads/pass/ >MAP006-1_2D_pass.fastq

NOTE one could also use the MiSeq PE 2x300 dataset available here (Oct 2014): http://systems.illumina.com/systems/miseq/scientific_data.ilmn

Many thanks to Ben Langmead for making this available as part of teaching material for his computational genomics class. As the code was released under a GNU GPL license, the DeBruijnGraph.ipynb IPyhton notebook is also released under the same license. Modified from http://nbviewer.ipython.org/github/BenLangmead/comp-genomics-class/blob/master/notebooks/CG_deBruijn.ipynb