…with the wrong orientation if a unique walk is found between the contig pair with orientation opposite to that of the link.
…d that suffixes with the same string were sorted by read name when they are actually sorted by position in the file. Thanks to Tomas Larsson for the bug report and test data.
…er than the k-mer size. The homopolymer and complexity checks are now disabled by default.
…M format if the --sam option is given. This replaces --description-file.
… in the FM-index.
…e scaffolding component.
…ffold pipeline requires (astat, bam2de).
…dle long (150+) reads.
… the SequenceProcessFramework to use a generic generator object.
… subprogram for cluster-extend.
…n the kmer length. Thanks to Dan Hughes for the bug report and test case.
…now returns a trimmed alignment to avoid bad-tails of the long reads.