Multiple Genome Sequence Aligner

This work is in progress and not ready for public consumption. Trying to use this code is strongly discouraged.

Setup

• config.py - edit this to paths appropriate for your system

Dependencies

Tests

Run test.sh

Included Files

• init.py

• batch_plot.py - some example plotting routines

• build_repeated_fasta.py

• evaluate.py

• evaluate_reads.py

• find_repeat_probability.py

• find_repeats.py

• find_repeats_large.py

• generate_all_reports.py - builds all plots used in the final report

• generate_consensus.py

• generate_mutation.py

• generate_reads.py

• generate_vcf.py

• helpers.py

• main.py

• mapper.py - a naive, simple aligner

• mapper_selector.py - runs an aligner

• mgsa.py - multi genome sequence aligner

• pipeline_batch.py - start a batch of tests specified by the provided batch config file

• pipeline_test.py

• sam_to_vcf.py

• ui.py - web based user interface

• wgsim_pipeline.py

• batch/ - batch files that run multiple alignment tests

• bio/ - common bio classes

  • bio.py
  • fasta.py
  • init.py
  • report.py
  • sam.py
  • vcf.py

• out/ - results of alignment tests

• state/ - details of current web based session

• static/ - included static files for the web based UI

• tests/

Deprecated

• cmd.py - command line based interface

Pipeline Config Files

Example Usage

Pipeline

• python pipeline_batch.py batch/pipeline_batch_bias_ecoli_2.cfg out/pipeline_batch_bias_ecoli_2.cfg

Deprecated

python cmd.py -s ../data/tiny_r1.fastq ../data/tiny_r2.fastq -g ../data/tiny_reference.fasta