BASIC v1.5.1

BASIC is a semi-de novo assembly method for assembling BCR and TCR genes from single cell RNA-seq data.

Changes since v1.5.0

This is a minor update that suppresses unnecessary Bowtie 2 output.

BASIC v1.5.0

BASIC is a semi-de novo assembly method for assembling BCR and TCR genes from single cell RNA-seq data.

Changes since v1.4.1

• An optional --subsample argument has been added that enables subsampling to <int> number of input reads when assembling.
• Code has been refactored and linted to enable more thorough testing and to more easily catch configuration errors.

BASIC v1.4.1

BASIC is a semi-de novo assembly method for assembling BCR and TCR genes from single cell RNA-seq data.

Changes since v1.4.0

• The output directory (-o) can now be specified as an absolute path
• The exit code for BASIC is now 1 instead of 0 in the case of various errors
• TCR assembly names now contain TRA or TRB rather than heavy or light

BASIC v1.4.0

BASIC is a semi-de novo assembly method for assembling BCR and TCR genes from single cell RNA-seq data.

Command line argument updates and additions:

The following backwards-compatible changes have been made:

• New: -t for specifying a temporary directory. May be potentially useful in a cluster environment in order to write intermediate files to scratch storage
• New: -a for allowing partial receptor reconstruction if reads do not map to one or both chains
• Updated: -b (path to Bowtie2) now accepts the absolute path to the Bowtie2 executable or the directory containing it

Other changes since v1.3.1

• Travis CI has been added to test BASIC with single- and paired-end reads on Linux and macOS
• Argument help messages have been improved when running BASIC.py -h
• The multiprocessing approach has been refactored to collect all Process results then write out final fasta
• The README has been updated to include installation instructions and more comprehensive usage information

BASIC v1.3.1

BASIC is a semi-de novo assembly method for assembling BCR and TCR genes from single cell RNA-seq data.

Key features in BASIC (1.3.1):

• BASIC can now assemble both BCR and TCR sequences.
• BASIC can now assemble BCRs and TCRs using reads of different lengths, which may arise from read trimming.
• Includes bug fixes and speed improvements.
• Has a new /db structure and flag that allows easy implementation of new species-specific BCR and TCR assemblies.

User Guide:
http://ttic.uchicago.edu/~aakhan/BASIC/

Contact:
Please contact Aly Khan (aakhan@ttic.edu) for any questions or comments.
More recent updates to BASIC have been contributed by Derek Croote (dcroote@stanford.edu).