ngs_mapper

Version: 1.3.0

The ngs_mapper is a configurable pipeline next generation sequence pipeline that aims to be easy for the bioinformatician to install as well as use. It focuses on documentation as well as easy configuration and running. The pipeline is also meant to get you from data to completed genome as easy as possible.

The documentation is a work-in-progress as the aim is to keep it as much up-to-date as possible with the pipeline as it changes. If anything seems out of place or wrong please open a bug report on github

Changelog

Version 1.3.0

  • Added ngs_filter stage/script that can filter based on index fastq files as well as reads that contain an N. This stage is off by default.
  • Fixed a bug where some scripts were not logging properly

Version 1.2.4

  • Fixes documentation issue with umask for sync user

Version 1.2.3

  • Added travis-ci support to automatically run tests when code is pushed to github
  • Projects now default to running inside of a temporary directory inside of the specified output directory(-od)
  • runsample now sets TMPDIR to tmpdir inside of output directory so that all analysis is run within that directory

Version 1.2.2

  • runsample accepts –qsub_m and –qsub_l commands which will direct it to return a PBS qsub job that can be piped into qsub
  • Added Python 2.6 support

Version 1.2.1

  • Removed all occurances of bqd.mpileup and replaced with samtools.mpileup
  • Changed bqd.parse_pileup such that it utilizes samtools.MPileupColumn to generate the dictionary items
  • Remove legacy BamCoverage code that is not used anywhere
  • Added support to select reads by specific platforms in runsample.py
  • Fixed bug where MiSeq Index reads were being included in the mapping
  • Renamed unpaired read file name that is produced by trim_reads from a generic Roche454 read name to simply unpaired_trimmed.fastq

Version 1.2.0

  • Added reflen to qualdepth.json files since length only told you the length of the assembly and not the reference.
  • Fixed issue where coverage graphic was not drawing gap lines at the end of references because there was no data.
  • sample_coverage colors were hard to distinquish so they were changed
  • Bug with sample_coverage where certain combinations of # of references and # of samples would generate a graphic where sub-plots for each reference were overlapping
  • Fixed incorrect command in doc/README.rst for how to open documentation with Firefox
  • Fixed issue with sample_coverage’s usage statement and arguments description
  • Fixed issue when no reads mapped and graphsample.py would raise an exception
  • Fixed an issue when there were directories inside of the path specified that contains read files
  • Replaced all .py scripts with same name but without .py. This is the correct way to have binary scripts for python. Aka, runsample.py is now just runsample

Version 1.1.0

  • Documentation updates
  • Platforms now identified via identifiers inside read files instead of filenames
  • IonTorrent sync added
  • Various bug fixes
  • base_caller.py can now utilize multiple processes to speed up analysis
  • Documentation now installs with the pipeline
  • run_bwa no longer makes temp directory but instead uses output path

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