Torsten Seemann

* `make again` * how to add/remove isolates

Support ERR and SRR accessions in the input table

1

It would be pretty slick if you could put `ERR6782346` in the `input.tab` file and it downloaded it from ENA as a dependency in the `Makefile` chain!

Like Wombac did so they can be put in the tree.

eg. Ion Torrent

Might make relationships clearer, dendrogram is misleading.

This will make it easier to find distances between near clones as they will be closer in the matrix.

Estimate genome size automatically

8

In my assembler `shovill` i estimate the genome size from kmer frequencies and use that to subsample the reads to a fixed coverage (100x) much like rasusa does: https://github.com/tseemann/shovill/blob/master/bin/shovill#L145-L175 Would...

Compiling fastANI on macOS but using gcc (solved)

2

``` ==> make install g++-8 -O3 -DNDEBUG -std=c++11 -Isrc -I /usr/local/opt/boost/include -fopenmp -mmacosx-version-min=10.7 -stdlib=libc++ -DUSE_BOOST src/cgi/core_genome_identity.cpp -o fastANI /usr/local/opt/boost/lib/libboost_math_c99.a -lstdc++ -lz -lm g++-8: error: unrecognized command line option '-stdlib=libc++' make:...

Is only one of boost or gsl needed?

2

I have a feeling boost gets used in priority over gsl? If so, which would make fastANI fastest? Or are both used?