• Release version 1.1.0
• Integrates 'ARKS' code (https://github.com/bcgsc/arks) into ARCS
  • Now, can run ARCS in either default mode (using linked read alignments) or ARKS mode (using exact k-mer mapping)
  • added --arks option to run in ARKS mode
  • Updated arcs-make to specify in which mode to run the scaffolding with linked reads
• Bug fix to calculation of barcode multiplicity

Big fixes
Improved documentation
Better input error handling

• Fix whitespace errors in makeTSVfile.py

• Do not trim lower-case characters from the ends of sequences.

• Use BX tag by default if present. The option --bx now has no effect.
• Read the FASTA sequence lengths from the SAM header.

• added --bx option to parse Chromium barcodes from BX tag
• fixed makeTSVfile.py for improved handling of distance
  estimates in LINKS v1.8.6 or later. The ARCS --dist_est
  option must be turned on for distance estimates to be generated
  and used downstream by LINKS.
• fixed incorrect default value of --end_length (0 => 30000)
• fixed --graph option to output vertex declarations in
  same order as input FASTA (ABySS compatibility fix)

• Release version v1.0.1
• added --dist_est option to estimate gap sizes
  • distance estimations are based on number of shared Chromium barcodes between contig head/tail regions that flank the gap
• added unit tests (make check)
• added --tsv option to output graph in TSV format
• added --barcode-counts option to output number of
  reads per barcode in TSV format