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ruanjue / wtdbg2

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly
GNU General Public License v3.0
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adjustable parameters with --load-alignments #255

Open rwhetten opened 1 year ago

rwhetten commented 1 year ago

Thanks for a great tool! I'm interested in optimizing assembly results by testing a range of parameter settings, using a single $prefix.alignments.gz file as input with the --load-aligments option. Is there a list of which parameters are used only during the alignment phase, and which are used after alignments are complete? Issue #4 mentions the --edge-min parameter, and issue #218 mentions --aln-dovetail and -s parameters as examples of options that can be changed when using --load-alignments. It would be helpful to have a complete list of parameters that can be optimized using an existing set of alignments, as well as a list of the parameters that are only used during alignment.

ruanjue commented 1 year ago

Most of filter parameters for alignments can used after load, such as --aln-min-match , --aln-min-similarity and many. The parameters --node-len and following (see help) are used in graph building and cleaning, work too.

rwhetten commented 1 year ago

Must the --dump-kbm command be used to save a file to be loaded with --load-alignments, or can the ${prefix}.alignments.gz file produced by the program be used directly? When I use the command wtdbg2 -p 19 -AS 2 -s 0.1 -g 16g -t 8 -fo test --load-alignments ${prefix}.alignments.gz I get the response ERROR: please specify the input with -i/--load-seqs/--load-kbm. What is the correct syntax for loading alignments?

ruanjue commented 1 year ago

Both of --load-seqs and --load-kbm are ok. -i is the short of --load-seqs.