PHYLO_PIPELINE

NAME

phylo_pipeline - Phylo Pipeline of PALEOMIX suite

SYNOPSIS

paleomix phylo_pipeline <command> [options] [makefiles]

DESCRIPTION

The PALEOMIX pipelines are a set of pipelines and tools designed to aid the rapid processing of High-Throughput Sequencing (HTS) data: The BAM pipeline processes de-multiplexed reads from one or more samples, through sequence processing and alignment, to generate BAM alignment files useful in downstream analyses; the Phylogenetic pipeline carries out genotyping and phylogenetic inference on BAM alignment files, either produced using the BAM pipeline or generated elsewhere; and the Zonkey pipeline carries out a suite of analyses on low coverage equine alignments, in order to detect the presence of F1-hybrids in archaeological assemblages. In addition, PALEOMIX aids in metagenomic analysis of the extracts.

The pipelines have been designed with ancient DNA (aDNA) in mind, and includes several features especially useful for the analyses of ancient samples, but can all be for the processing of modern samples, in order to ensure consistent data processing.

phylo_pipeline is the phylo pipeline of paleomix(1).

OPTIONS

Commands

phylo_pipeline help

Display this message.

phylo_pipeline example [...]

Copy example project to folder.

phylo_pipeline makefile

Print makefile template.

phylo_pipeline genotype [...]

Carry out genotyping according to makefile.

phylo_pipeline msa [...]

Carry out multiple sequence alignment.

phylo_pipeline phylogeny

Carry out phylogenetic inference.

Optional arguments

--version

show program’s version number and exit

-h, --help

show this help message and exit

--to-dot-file=DOT_FILE

Write dependency tree to the specified dot-file.

Progress reporting

--progress-ui=PROGRESS_UI

Select method for displaying the progress of the pipeline: ’running’ = Display only currently running nodes; ’progress’ = Display changes in state; ’summary’; one-line summary only. [Default is ’running’]

--ui-colors=UI_COLORS

Enable, disable, or force the use of color codes when printing the command-line UI. Unless forced, colors will only be printed if STDOUT is a TTY [Default is ’on’]

Logging

--log-file=LOG_FILE

Create the specified log-file and write any messages to this file. By default, a log-file will be generated in the folder specified using --temp-root, but only when messages are logged

--log-level=LOG_LEVEL

Log messages to log-file at and above the specified level; one of ’info’, ’warning’, ’error’, or ’debug’ [warning]

Scheduling

--samtools-max-threads=SAMTOOLS_MAX_THREADS

Maximum number of threads to use when genotyping or building pileups [1]

--examl-max-threads=EXAML_MAX_THREADS

Maximum number of threads to use for each instance of ExaML [1]

--max-threads=MAX_THREADS

Maximum number of threads to use in total [4]

--dry-run

If passed, only a dry-run in performed, the dependency tree is printed, and no tasks are executed.

Required paths:

--temp-root=TEMP_ROOT

Location for temporary files and folders [/tmp/USERNAME/phylo_pipeline]

--samples-root=SAMPLES_ROOT

Location of BAM files for each sample [./data/samples]

--regions-root=REGIONS_ROOT

Location of BED files containing regions of interest [./data/regions]

--prefix-root=PREFIX_ROOT

Location of prefixes (FASTAs) [./data/prefixes]

--refseq-root=REFSEQ_ROOT

Location of reference sequences (FASTAs) [./data/refseqs]

--destination=DESTINATION

The destination folder for result files [./results]

Files and executables:

--list-input-files

List all input files used by pipeline for the makefile(s), excluding any generated by the pipeline itself.

--list-output-files

List all output files generated by pipeline for the makefile(s).

--list-executables

List all executables required by the pipeline, with version requirements (if any).

Config files:

--write-config-file

Write config using current settings to $HOME/.paleomix/phylo_pipeline.ini

SEE ALSO

paleomix(1)

AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.