Captus v1.1.0

New in the assemble module:

• Contig depth of coverage is now calculated by mapping the reads back to the contigs using Salmon right after the assembly with MEGAHIT. This is now the default behavior unless --disable_mapping is enabled.
• The assembly is then automatically filtered by depth of contig, if --disable_mapping is used then only contigs with depth of coverage >1x are retained, otherwise contigs with depth of coverage >=1.5x are retained. The filtering threshold can be changed with --min_contig_depth.
• To replicate the behavior of previous versions use --disable_mapping and --min_contig_depth 0.
• The filtering can be repeated with --redo_filtering, without the need to reassemble, to try different values for --max_contig_gc and --min_contig_depth.
• The assembly HTML report has been completely rewritten to reflect these changes.

New in the extract module:

• Options --nuc_depth_tolerance, --ptd_depth_tolerance, --mit_depth_tolerance, and --dna_depth_tolerance allow to filter contigs by depth of coverage during locus extraction. Among the contigs with hits to a particular marker type (e.g., nuclear), the median of the depths of coverage is calculated and this tolerance factor is used to determine the minimum (median / tolerance) and maximum (median * tolerance) depth allowed. The depth of coverage is taken from the contig names when they contain the pattern _cov_X.XX_.
• To replicate the behavior of previous versions use --ignore_depth.
• Added option --disable_stitching. By default, Captus recover a locus across multiple contigs, this option forces the recovery of a locus in a single contig (for example when providing chromosome-level genome assemblies).

Other improvements or additions:

• The accessory script filter_most_common_target_per_locus.py creates a new reference target file with only the most common target per locus found during the extraction step. This new reference target set can be used to re-extract the loci and potentially improve the informed paralog filtering.
• All the reports have been updated to include the version and command of Captus used.
• Updated installation instructions and documentation.
• Some long output filenames have been shortened.

Captus v1.0.1

• During assembly of hits when extracting a miscellaneous DNA reference target, the delta in identity percentage between two hits to be considered compatible has been reduced from 5% to 3.33%, initial test indicate slight improvement in recovery.
• In some edge cases, when translating a CDS reference target set, the same nucleotide sequence can produce perfectly translated protein in more than a single reading frame, we give now priority to positive reading frames in case of a tie.
• Latest pandas versions introduced breaking changes, we provide a fix.
• When creating a new miscellaneous DNA reference from clustering, each target sequence in a reference locus can have different strands. We add a method to uniformize the strand per reference locus.
• Added an option to the align step to --only_collect the extracted markers and exit afterwards (requested by Diego Morales)
• Fixed multiple small bugs.

Captus v1.0.0

• Additional improvements to captusd bait: added options --min_expected_tiling and --remove_ambiguous_loci for the creation of baitsets and their corresponding reference target files.

Captus v0.9.99

• Now any BUSCO lineage database can be used as reference target file, just download a .tar.gz from https://busco-data.ezlab.org/v5/data/lineages/ and provide the file path for Captus extraction
• Added shortcut for captus_assembly as simply captus (data assembly)
• Added entry point for captus_design and a shortcut as captusd (bait design)
• The cluster step of bait design now reports mean number of copies per locus instead of just classifying it as single- or multi-copy
• Added a function to create a reference target file (for locus extraction) after bait clustering and tiling
• Code cleanup and minor cosmetic changes

Captus v0.9.98

• Fixed potential problem with recognition of _R1. or _R1_ patterns in filenames
• Support for FastQC v0.12.1 update (s-andrews/FastQC@fbd9cf5)
• Speed up QC step during cleaning step
• If the user provides a clustering threshold with --cl_min_identity then the miscellaneous DNA extraction is performed using the same identity.
• Allow decimals in maximum average number of copies in a cluster via --cl_max_copies
• Minor cosmetic improvements

Captus v0.9.97

• Fixed a bug in the extraction report happening when the extraction statistics tables are not sorted. This bug doesn't affect the output at all, just the report heatmap.

Captus v0.9.96

• Fixed indentation bugs that prevented Falco or FastQC from running during the clean step and the subsampling of reads during the assemble step
• Secret feature, coding genes databases can also be extracted as nucleotide
• Code cleanup and minor fixes

Captus v0.9.95

• Updated perl dependencies, now the latest bioperl and yaml can be used by Scipio
• Improved Scipio parallelization, assemblies sorted by size in decreasing order before processing
• Reduce maxIntron search for Scipio to 50000bp (previous settings took too long and created unlikely gene models when chromosome-level assemblies are analyzed)
• Code cleanup and multiple cosmetic changes

Captus v0.9.93

• Fixed bugs found in extract.py during clustering (Thanks to Lydia Paradiso)

Captus v0.9.92

• Added module for bait design
• To see help on the new module use captus_design --help