Cider v0.8.0

Functional improvements:

• Add NO_HIGH_QUAL_SUPPORT soft filter.
• By default, any read with more than 10% bases with low base quality are discarded.
• Change poly G trimming threshold from 6 or more consecutive Gs to 2.
• Remove reads where > 10% of the bases are low quality.

Speed improvements:

• Use multiple threads when building layouts.
• Implementing progressive sealing of nodes in the tree layout.
• Improve performance of VJ layout joining. First use common read IDs, then use 8 base word hash to find candidates. The word hashes were generated from the base after V anchor, and up to the base before J anchor.
• By default, downsample reads if number of reads exceed 600k for a gene.

New Arguments:

• New command line argument: max_low_qual_base_fraction.
• New command line argument: max_reads_per_gene.