fdstools 2.1.1

Forensic DNA Sequencing Tools

Forensic DNA Sequencing Tools

Tools for filtering and interpretation of Massively Parallel Sequencing data of forensic DNA samples. To obtain a list of included tools with a brief description of each tool, run:

fdstools --help

For a complete description of a specific tool and its command line arguments, run:

fdstools --help TOOLNAME

Installation

FDSTools requires Python version 3.5 or later.

The recommended way to install FDSTools is by using the pip package installer. If you have pip installed, you can easily install FDSTools by running the following command:

pip install -U fdstools

Alternatively, FDSTools can be installed by running:

python setup.py install

Release Notes

Version 2.1.1 (2024-07-02)

Fixed an issue that caused the new [flank_length] section to be ignored.

TSSV no longer requires [flanks] to be specified for explicitly-defined non-STR markers if the ending [genome_position] is provided.

Version 2.1.0 (2024-04-30)

Updated STRNaming nomenclature to version 1.2. Please note that this is a backwards incompatible update: this version of FDSTools is unable to correctly interpret allele names that were produced with a prior version! Please see https://fdstools.nl/strnaming/updates for more information.

Changed interpretation of the [flanks] section in the library file: it can no longer contain numbers, but the value 'REF' can be specified to indicate that GRCh38 reference sequence should be used (which was already the default). A new [flank_length] section is introduced to allow specifying marker-specific minimum and maximum (or exact) flanking sequence length; the value specified for TSSV's -L/--flank-length option is then clamped between these values. If a [flanks] section is present and contains a short sequence (possibly with IUPAC codes), it is implicitly extended with GRCh38 reference sequence to the requested length by TSSV.

To use TSSV with explicitly-defined markers, those markers now also require specifying flanks explicitly. Previously, since FDSTools v2.0.0, TSSV's behaviour regarding these markers was erratic.

Greatly improved handling of microhaplotype markers, and we finally introduced the first suite of component tests, covering Allelefinder, Seqconvert, Stuttermark and TSSV. Welcome to the team, Brechtje!

Version 2.0.4 (2023-03-02)

Microhaplotype alleles with SNPs adjacent to any of the microhaplotype positions are now recognised. For example, an allele previously named "MH_N_123NC>GA" will now be named "MH_G_124C>A" instead.

Greatly improved loading speed for large library files.

Version 2.0.3 (2022-08-27)

Added NimaGen IDseek OmniSTR built-in library file (ID-OmniSTR).

Version 2.0.2 (2022-07-25)

Fixed a compatibility issue with Python 3.10, that caused TSSV to crash. Fixed some issues that could cause crashes in the Pipeline tool.

Corrected the reported range of AmelongeninY in the ForenSeq-A and ForenSeq-B library files which were introduced in v2.0.1, by adding 1 to the starting position. The range is now identical to the UAS Flanking Region Report range. If still you need to work with data previously generated using the ForenSeq-A or ForenSeq-B library as shipped with v2.0.1, use the Library tool to obtain a copy of the built-in library file and make sure the range of AmelongeninY starts at 6869870.

Version 2.0.1 (2022-05-12)

Added support for microhaplotype targets. For markers configured as such, the 'allelename' sequence format will look like "MH_AGGTC".

Added ForenSeq DNA Signature Prep Kit library files with ranges specifically optimized for FDSTools (often longer than UAS Flanking Region Report).

Version 2.0.0 (2021-07-15)

Transition to Python 3.5, along with a major upgrade to all tools to provide an overall better experience.

Allele naming is now handled by STRNaming, eliminating the need for complex library files. Library files of commonly-used kits are built in.

Kits that sequence a target on a single strand (such as the ForenSeq DNA Signature Prep Kit by Verogen) are now supported.

Version 1.2.1 (2021-07-15)

This release focuses on finishing support for Python2 before the transition to Python3. FDSTools will now display the help page if no command is given. A message about the transition to Python3 in the next version of FDSTools is added to the command-line help pages. Furthermore, dependency version numbers have been updated to ensure smooth installation on Python2 as well as a smooth transition to Python3.

Version 1.2.0 (2019-03-29)

Major improvements and fixes to the TSSV tool. Most notably, it no longer relies on the external tssvl program because that is no longer compatible with FDSTools. Furthermore, the new TSSV tool v2.0.0 comes with a major performance upgrade and has some updated command-line arguments.

This release also fixes an issue in Samplestats and adds the ability to apply graph filtering before noise correction in Samplevis, making the effects of noise correction more apparent.

Version 1.1.1 (2017-03-15)

Fixeds incorrect calculation of tLeft, fLeft, rLeft, tRight and fRight columns in the report output file of TSSV, when -T/--num-threads was set to 2 or higher. The primary output was unaffected.

Version 1.1.0 (2017-03-14)

In STR allele names for sequences that don't exactly match the description given in the library file, no more insertions are produced at the end of the prefix or the beginning of the suffix, in favour of extra STR blocks.

Empty input files and broken pipelines are now handled gracefully across all tools. Specifically, an empty input file is now treated as if the expected columns existed, but no lines of actual data were present. This greatly helps in tracking down issues in pipelines involving multiple tools, as tools will now shutdown gracefully if an upstream tool fails to write output. Only the failing tool will output an error.

Furthermore, a new option has been added to the TSSV tool, enabling multithreading support. This can greatly reduce analysis time by using more (or all) cores of the system's processor simultaneously.

Finally, various small bugs and glitches were fixed.

Version 1.0.1 (2016-12-21)

FDSTools library files may now contain IUPAC ambiguous bases in the prefix prefix and suffix sequences of STR markers (except the first sequence, as it is used as the reference). Additionally, optional bases may be represented by lowercase letters.

An option was added to the Pipeline tool to skip running Allelefinder, using a user-supplied allele list file instead. Multiple options have been added to the Vis tool and some have been regrouped to more easily find the option you are looking for.

It is now possible to save the a Samplevis HTML visualisation after having made changes, preserving the changes made.

And various minor bug fixes and improvements throughout.

Version 1.0.0 (2016-10-03)

Fixed an issue with variant descriptions in allele names of non-STR markers that made it impossible to convert those back to raw sequences.

Added various useful options. Most notably, Samplevis now displays a tooltip when the mouse pointer is over an allele, providing various details about that allele.

And various minor bug fixes.

Version 0.0.5 (2016-09-06)

Added the Library tool, for creating a template library file that includes helpful commentary and examples to get new users started. Creating an empty library file used to be a somewhat confusing option in the Libconvert tool. Also, the Blame tool was replaced with the more advanced BGAnalyse tool.

Added the Pipeline tool, which implements some ready-made pipelines involving most of the other tools in FDSTools. Three pipelines are provided: one for noise reference sample analysis, one for case sample analysis, and one for generating a background noise database from the reference samples.

In Samplestats, the default allele calling option thresholds have changed: - Changed default value of -m/--min-pct-of-max from 5.0 to 2.0 - Changed default value of -p/--min-pct-of-sum from 3.0 to 1.5

The TSSV tool was updated with an option to increase the penalty given to insertions and deletions in the flanking sequences. It now requires TSSV version 0.4.0 to be installed.

Various upgrades to visualisations, bringing a new responsive design to all HTML visualisations and fixing various issues.

Version 0.0.4 (2016-07-26)

Improved debugging: FDSTools will now print profiling information to stdout when the -d/--debug option was specified. Also, all tools now correctly interpret '-' as the output filename as 'write to standard out'.

BGEstimate has gained a new option to require a minimum number of unique genotypes in which a specific allele must have been seen before it will be considered for noise estimation. This is to avoid 'contamination' of the noise profile of one allele with the noise of another. If homozygous samples are available for an allele, this filter is not applied to that allele.

Reduced the memory usage of BGPredict and BGMerge. Also, BGPredict will now output nonzero values below the threshold set by -n/--min-pct if the predicted noise ratio of the same stutter on the other strand is above the threshold. Previously, values below the threshold were clipped to zero, which may cause unnecessarily high strand bias in the predicted profile. Similarly, by default Stuttermodel will no longer output a fit on one strand if no fit could be optained on the other strand.

Changes have been made to rounding and column order in Samplestats.

Various minor fixes and enhancements have been made, mostly to the visualisations.

Version 0.0.3 (2016-02-02)

First version of FDSTools with all strings attached. Introduces 15 new tools and five visualisations.

In Stuttermark, the column names 'name' and 'allele' have been changed to 'marker' and 'sequence', respectively, reflecting those of all the other tools. WARNING: Stuttermark is now INCOMPATIBLE with output from TSSV, but made compatible with TSSV-Lite and the new, bundled TSSV tool instead.

Version 0.0.2 (2015-07-23)

Added a new global option: -d/--debug. This option disables the suppression of technical details that would normally be visible when an error occurs.

Stuttermark now accepts raw sequences and allele names as input, which are automatically rewritten as TSSV-style sequences using a specified library file. Also, the 'name' column is now optional.

Version 0.0.1 (2015-07-02)

Initial version of FDSTools, featuring a single tool: Stuttermark v1.3.