Falco v2.0

New features:

• Added 2 new analysis modes - alignment-only and transcript assembly
  • Alignment-only mode is designed to output alignment files (in BAM format) for each samples
  • Transcript assembly mode is designed for performing transcript assembly from input samples to create an updated reference annotation
• Added Python3 support to all analysis modes (including Quantification analysis mode) and made PySpark use Python3 by default
• Added support for using custom AMI when launching EMR cluster (require EMR release >= 5.7)

Note: The default directory for application have now been set to /app rather than /mnt/app in order to support custom AMI when launching EMR cluster

Falco v1.1

New features:

• Added HISAT2 and HTSeq as possible option for alignment and quantification tool

Bug fixes:

• Fixed a bug with single-ended file handling in pre-processing streaming script
• Fixed emr job submission command to deal with complex extra arguments for aligner and counter

Falco v1.0

Initial release of Falco.