Jue Ruan

Dear Ryan R. Wick and Kathryn E. Holt, Wtdbg2 aims to provide a quick solution for long reads assembly, it often leave the polishing step to other tools, like quiver/pilon....

Add `-R`, try `--aln-dovetail -1` or `--aln-dovetail 1024`, also `-l 6000`. You can fast load alignments by `--load-alignments`, then increase `-s` and `-l` to build assembly graph.

wtdbg2 doesn't check that, but you can view the assembly from `.ctg.dot` (graphviz format).

Please have a look at http://graphviz.org/, you can convert it into a pdf file using `dot -Tpdf -O .ctg.dot`.

On sensitivity, kmer-psize is better. On specificity, kmer-fsize is better. It is allowed to use `-k 2 -p 19` to get a bit more specificity b ut less sensitivity than...

Because it didn't provide `VERSION=2.5` in the compilation. But I am not sure what happened in conda.

bc1018.ctg.dot contained all contigs, but wtdbg2 only reported larger contigs, please see `wtdbg2 --help` for '--ctg-min-length' and `--ctg-min-nodes`.

Ok, I see. the lengths in ctg.dot is counted in BINs (256bp). I have modified wtdbg-dot2gfa.pl, see https://github.com/ruanjue/wtdbg2/commit/e9ab08b989504721250a89f89cedfcc6e495416a

FASTA is more convenient for users. BTW, I am developing the next version of wtdbg, will consider to offer an option to output GFA instead of FASTA. Thanks for your...

你把运行日志发到我邮箱吧 [email protected]