pilon

Pilon version 1.24 has one algorithm change which affects local reassembly solutions, particularly when using diploid data. Previously, if there were several equivalent solutions for a local reassembly (gap fill or continuity break fix), it would pick the first available solution. In v1.24, it picks the smallest change among equivalent alternatives, preventing it from including surrounding heteroz...

Pilon version 1.23 introduces two new experimental arguments to specify long read input BAMs:

--nanopore ont.bam identifies ont.bam as containing long reads from Oxford Nanopore sequencing --pacbio pb.bam identifies pb.bam as containing long reads from Pacific Biosciences sequencing

In this version, the long read BAMs are only used for SNP and indel calling based on pileups. Long re...

This is a very minor release incorporating two bug fixes reported by users:

1. Fixed bug in .bed file coordinates generated by the --tracks option (start coordinate was 1-based rather than 0-based);
2. More flexibility in --target specifications is now allowed so that scaffold names may contain colons (apparently Quiver generates these). Thanks to bwlang for sample code!

There should...

Version 1.21 introduces two new --fix options for assembly improvement: snps and indels. Prior to this release, the bases fix option was used to control alignment-based (as opposed to assembly-based) fixes of both SNPs and small indels. Now, fixing of SNPs and small indels can be controlled independently. The --fix bases option is retained for back-compatibility, and is equivalent to spe...

This release only fixes a bug in the experimental PacBio long read circular element closure feature introduced in 1.19.

--bruce, 20 Sep 2016