nanoPARE tools v1.1

A number of bugs were fixed to improve performance and make the pipeline compatible with more Linux environments.

-- FASTQ commandline tools were updated for compatibility with Python 3+.
-- Bedgraphs are stored in numpy arrays for improved memory efficiency in larger genomes.
-- Added arguments --gtf_gene_tag and --gtf_transcript_tag in nanoPARE_setup.sh for more options in parsing GTF annotations.
-- Improved parsing of annotations in the GFF3 format.
-- Fixed a bug where empty lines in a FASTQ file resulted in a crash.

nanoPARE analysis tools (manuscript release version)

nanoPARE analysis tools v1.0

This release version contains versions of the code used in the article Schon, Kellner, et al., "nanoPARE: Parallel analysis of RNA 5′ ends from low-input RNA."