Scripts

contig_stats.pl

contig-stats.pl is a Perl script that will automatically describe features of a sequence assembly.

makereads.py

Randomly generates reads to aid in the testing of alignment programs. Reads are made from randomly reading chunks from the input fasta sequence. Can simulate heterozygous/polyploid reads, as well as paired-end reads.

BPstats.py

Performs and outputs various statistical tests for each contig in a GSS basepile output. it is assumed that the information for each contig is 1000 bases long.

gapstrip.py

Removes all of the gaps (i.e. '-') that are common (i.e. at the same index) to all of the sequences in an aligned FASTA file. By default, the first sequence is considered the reference and is excluded from the analysis, but the number of sequences that are treated as such can be changed.

sumqual.py

A script used in conjunction with the free aligners NUCmer and the free short read assembler YASRA. Creates a file with a similar to the format to that of the .qual file YASRA outputs, except each base can have multiple sets of quality values.

runyasra.py

Runs the free short read aligner YASRA and organizes its output into a folder. Links to the input data are also saved in the output folder.

alignreads.py

A pipeline for combining the free aligner NUCmer and the free short read assembler YASRA so full alignments can be made with one command. Alignreads uses the following scripts from the Liston lab: runyasra.py, sumqual.py, and qualtofa.py.
Note: For use with the older versions of YASRA.