Minnesota Supercomputing Institute
With regards to the safety measures put in place by the university to mitigate the risks of the COVID-19 virus, at this time all MSI systems will remain operational and can be accessed remotely as usual. The only planned outages concern our in-person Helpdesk and tutorials. More information, as well as alternative remote support options, can be found at MSI COVID-19 Continuity Plan
0.26, 0.28, 0.28.1, 0.35.0
Thursday, February 27, 2020
From the breseq manual pages:
breseq (pronounced: breeze-seq) is a computational pipeline for the analysis of short-read re-sequencing data (e.g. 454, Illumina, SOLiD, etc.).
It uses reference-based alignment approaches to predict mutations in a sample relative to an already sequenced genome. breseq is intended for microbial genomes (<10 Mb) and re-sequenced samples that are only slightly diverged from the reference sequence (<1 mutation per 1000 bp).
breseq‘s primary advantages over other existing software programs are that it can:
Predict new sequence junctions, such as those associated with mobile element insertions, from single-end read data.
Reliably identify short indel mutations by appropriately masking the ends of read alignments.
Produce annotated output describing biologically relevant mutational events.
module load breseq
This loads breseq, bowtie and R.
>>>breseq -r NC_012967.gbk SRR030257_1.fastq SRR030257_2.fastq