Description

This tool generates a contig map file using the information from a NCBI assembly report. It has an option to select which column in the NCBI report should be used.

Installation

NcbiReportToContigMap requires Java 8 to be installed on your device. Download Java 8 here or install via your distribution's package manager.

Download the latest version of NcbiReportToContigMap here. To generate the usage run:

java -jar <NcbiReportToContigMap_jar> --help

Manual

NcbiReportToContigMap needs a NCBI assembly report, an output file, and the name column that should be used from the report. All columns in the report can be used but these are the most common fields to choose from: - 'Sequence-Name': Name of the contig within the assembly - 'UCSC-style-name': Name of the contig used by UCSC ( like hg19 ) - 'RefSeq-Accn': Unique name of the contig at RefSeq (default for NCBI)

Optionally other columns in the report can be added to the contig map with the --names flag.

Example

To construct a contig map from a NCBI assembly report, use the UCSC-style-name for the contigs, and include the RefSeq-Accn column:

java -jar <NcbiReportToContigMap_jar> \
-a ncbi_assembly_report.txt \
-o contig_map.tsv \
--nameHeader UCSC-style-name \
--names Refseq-Accn

Usage

Usage for NcbiReportToContigMap:

Option Required Can occur multiple times Description
--log_level, -l no no Level of log information printed. Possible levels: 'debug', 'info', 'warn', 'error'
--help, -h no no Print usage
--version, -v no no Print version
--assembly_report, -a yes no Assembly report from NCBI
--output, -o yes no output contig map
--nameHeader yes no What column to use from the NCBI report for the name of the contigs. All columns in the report can be used but this are the most common field to choose from: - 'Sequence-Name': Name of the contig within the assembly - 'UCSC-style-name': Name of the contig used by UCSC ( like hg19 ) - 'RefSeq-Accn': Unique name of the contig at RefSeq (default for NCBI)
--names no yes (unlimited) Keys of the report to use in contig map

About

NcbiReportToContigMap is part of BIOPET tool suite that is developed at LUMC by the SASC team. Each tool in the BIOPET tool suite is meant to offer a standalone function that can be used to perform a dedicate data analysis task or added as part of a pipeline, for example the SASC team's biowdl pipelines.

All tools in the BIOPET tool suite are Free/Libre and Open Source Software.

Contributing

The source code of NcbiReportToContigMap can be found here. We welcome any contributions. Bug reports, feature requests and feedback can be submitted at our issue tracker.

NcbiReportToContigMap is build using sbt. Before submitting a pull request, make sure all tests can be passed by running sbt test from the project's root. We recommend using an IDE to work on NcbiReportToContigMap. We have had good results with this IDE.

Contact

For any question related to NcbiReportToContigMap, please use the github issue tracker or contact the SASC team directly at: sasc@lumc.nl.