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