BabrahamLinkON v0.2.0

Most changes pertain to the short pipeline. Moved main scripts into bin folder.

Precleaning

• The sequence beyond anchor is no longer removed from output reads.
• J end UMI moved from deduplication, so that all UMI extraction is now preformed at precleaning stage.
• Fixed comments in R script that caused J germline plots not to be produced.
• Check if germline plot is produced.
• Fixed an incorrect mispriming correction offset for the kappa locus.

Mispriming error estimate

• Extended error estimation for human sequences.

For short reads:

• json file written with identity of reads assembled and unassembled to allow merging after deduplication.

Deduplication

• Option to output sequences with ambiguous N nucleotides (normally these are filled in with basepairs from sequences best matching the consensus).
• Fixed bug in UMI report tables (most likely cause by pandas update).
• Simplified options, made MSA available to all pipelines.
• Moved general functions into deduplicattion_general.py and split deduplicate_bundle_parallel for clarity.
• Updated UMI correction to work with latest version.

Annotation and clone assembly

• Added json option so output reads can be marked assembled or unassembled.
• DJ reads are also filtered by the V end IgBlast calls, instead on just J end.

Setup

• Moved package data into MANIFEST.in to enable pip --editable mode to work with pkg_resources.resource_filename.

BabrahamLinkON v0.1

Initial release