A pipeline for combining the free aligner NUCmer and the free short read assembler YASRA so full reference guided alignments can be made with one command. Alignreads uses the following scripts from the Liston lab: runyasra.py, sumqual.py, and qualtofa.py. It also uses YASRA and its binaries, including lastz. It must be possible for the python interpreter to find these scripts to run alignreads; this can be done saving copies of scripts in the Python26 folder, your bin folder, or modifying your .chsrc file to search where they are saved on your system (necessary if lastz binaries cannot be found). Alignreads preserves almost all of the functionality and output of the five programs it uses, so there are many options (over 40). Because there are so many modifiers, the default help menu (obtained with 'python alignreads.py' ) only has the options used most often; to get all of the options type 'python alignreads.py -H' or 'python alignreads.py --advanced-help'. Since there are many files associated with the alignment, the output is a folder with numerous files organized into subfolders. Alignreads.py can also start the pipeline from a folder produced by a previous run of alignreads.py or runyasra.py. In that case, the output is saved in the input folder and separate subfolders are created for each alignment.
Version 2.25 can be loaded from the link below. The most recent version can be downloaded from github.
Reference the following paper in which it was first described:
Straub, S.C.K., M. Fishbein, T. Livshultz, Z. Foster, M. Parks, K. Weitemier, R.C. Cronn, A. Liston. 2011. Building a model: Developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing. BMC Genomics 12:211.