HybPiper version 2.1.6

• Intronerate is now run by default. The flag --run_intronerate for subcommand hybpiper assemble has been changed to --no_intronerate.
• If Intronerate fails, failed genes and errors will be printed and logged; the exonerate_contigs step of the pipeline will continue.
• Updated error handling and logging for the exonerate_contigs step of the pipeline.
• Change default DPI of heatmaps to 100 (previously 150) for hybpiper recovery_heatmap and hybpiper paralog_retriever
• Enforce rendering of all loci (x-axis) and sample (y-axis) labels in heatmaps; previously, matplotlib/seaborn would dynamically drop labels if they were too closely spaced.
• Added flags --no_xlabels and --no_ylabels for hybpiper recovery_heatmap and hybpiper paralog_retriever; turns off rendering of the corresponding labels in the saved figures.
• If the auto-calculated size of heatmaps for hybpiper recovery_heatmap and hybpiper paralog_retriever is greater than the maximum number of pixels (65536) in either/or length and height, resize the figure to 400 inches and 100 DPI. Note that large datasets can fail to render fully in the saved figure even if the pixel dimensions are less than the maximum (see e.g. https://stackoverflow.com/questions/64393779/how-to-render-a-heatmap-for-a-large-array), but reducing the size/DPI further allows the full figure to be rendered.
• Added module version.py for a single location of HybPiper version number.
• Print and log HybPiper version when calling all subcommands.
• Added column 'TotalBasesRecovered' to the hybpiper stats report, listing the total number of nucleotides recovered for each sample (not counting N characters). Added 'TotalBasesRecovered' as a filtering option in hybpiper retrieve_sequences.

HybPiper version 2.1.5

• Bugfix: fixed an issue in exonerate_hits.py that could result in initial Exonerate hits being trimmed too aggressively at their 3' ends.
• Bugfix: fixed an issue in exonerate_hits.py that could introduce minor insertions in to the supercontig (concatenated exon and partial intron) sequence used when running Intronerate.

HybPiper version 2.1.4

Bugfix: fixed an issue when using --run_intronerate that could cause an error and result in no *.FNA sequence being produced for some genes.

HybPiper version 2.1.3

v2.1.3

Update to 2.1.3

HybPiper version 2.1.1

Added hybpiper fix_targetfile command.

HybPiper version 2.0.2

First release for HybPiper version 2.

Final HybPiper 1.3 Version

Legacy version for Hybpiper 1.X, last updated March 2020.

Bug Fix Reverse Complement Sequences

Fixes #38

All users who recovered sequences with version 1.3 should re-run the exonerate step to recover sequences with the correct strand. Instructions can be found in the issue.

The Herbarium Update

1.3 The Herbarium Update January, 2018

Bug fixes and features related to the use of targeted sequencing from herbarium material. These samples tend to have short contigs that can cause issues when trying to assemble full-length genes.

Features

• Added --exclude flag to be the inverse of --target: all sequences with the specified string will not be used as targets for exon extraction (they will still be used for read-mapping). Useful if you want to add supercontig sequence to the target file, but not use it for exon extraction.

• Added --addN to intronerate.py. This feature will add 10 N characters in between joined contig when recovering the supercontig. This is useful for identifying where the intron recovery fails, and for annotation processing (i.e. for GenBank).

• Added a new version of the heatmap script, gene_recovery_heatmap_ggplot.R. This script is much simpler and produces nice color PNG images, but struggles a bit on PDF output. The original heatmap script is stil included. Thanks to Paul Wolf for the ggplot code!

Bug Fixes

• Fixed misassembly of supercontigs when there are multiple alignments to different parts of the same exon.
• Fixed poor filtering of GFF results to produce intron/exon annotation.
• Fixed non-propogation of exonerate parameters

HybPiper 1.2: Target Finesse, Unpaired Reads, and Python 3

Features

• Added --unpaired flag. When using paired-end sequencing reads, a third read file may be specified with this flag. Reads will be mapped to targets separately, but will be used along with paired reads in contig assembly.

• Added --target flag. Adds the ability to choose which of the reference sequences is used for each gene. If --target is a file (tab-delimited file with one gene and one target name per line), HybPiper will use that. Otherwise --target can be the name of one reference. HybPiper will only use targets with the specified name in the Alignment/Exon Extraction phase. All other targets for that locus will only be used in the Mapping/Read Sorting phase.

• Added --timeout flag, which uses GNU Parallel to kill processes (i.e. Spades or Exonerate) if they take X percent longer than average. Use if there are a lot of stuck jobs (--timeout 1000)

• Python 3 compatibility

Bug Fixes

• Can accommodate Solexa FASTQ paired headers
• Fixed spades_runner.py not recognizing --cpu on redos
• Prints more meaningful messages for some common errors
• Can accommodate prefix not being in current directory
• Deletes sorted reads on restart to prevent double counting reads.
• spades_runner.py will now respect --kvals
• Added initial call to log for reads_first.py