Shaun Jackman

Here you go: - ftp://ftp.bcgsc.ca/public/sjackman/hsapiens-graph.asqg.gz - ftp://ftp.bcgsc.ca/public/sjackman/hsapiens.scaf ``` sh sga scaffold2fasta -m 500 --write-unplaced --use-overlap -o hsapiens-scaffolds.fa -a hsapiens-graph.asqg.gz hsapiens.scaf ```

Any chance you've had some time to look into this issue, Jared?

No worries. I am sympathetic to time constraints. We wanted to include SGA in an assembly comparison of GIAB HG004. SGA will be included in the comparison of contigs. Including...

What's the format of the `.scaf` file? Perhaps I could use `MergeContigs` from ABySS as a hack work around to create the scaffolds FASTA file. ``` contig-6181580 contig-4954829,228,151.2,0,0,D contig-197051,2178,122.2,0,1,D ```

The format is: ``` c++ std::ostream& operator

Could I convert this to an ABySS path file like so, or is it not quite so simple? How do I convert the `Dir` and `Comp` components to a `+`...

Is the `.scaf` file the final list of which contigs go in which scaffolds with one scaffold per line, or is it a list of distance estimates that still need...

Can you give me a brief description of how to convert a SGA `scaf` file to an ABySS `path` file? If you are able to convert the following `.scaf` record...

No worries, Jared. Quick comments are helpful. We're including SGA in this comparison to ABySS 2.0 due to its low memory usage. We're also comparing to DISCOVARdenovo, and it yields...

Here's a hacktastic script to convert a SGA `.scaf` file to an ABySS `.path` file. Thanks for your help, Jared. ``` sh #!/bin/sh set -eu exec gawk -e ' !/\t/...