Torsten Seemann

Support single-end (SE) reads

4

Should Shovill support SE reads?

Add a nice [stats] section to end of shovill.log

1

Make it tab separated too. ``` [stats] \t contigs \t 141 [stats] \t totalbp \t 4235451 [stats] \t n50 \t 23444 ``` etc So it can be grepped and parsed....

Remove "nearly" poly-G contigs

1

Examples: ``` ATATTGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGAGGGGGGGGGGGG ```

Would be good to have clean names in the graph file to match the contigs. (the original contig name is in `origname=XXX` in the FASTA comment however, so it's not...

``` ln -s /dev/null blackhole.msh mash sketch -o blackhole -r R1.fq.gz ``` via @kloetzl

Add --fast mode

1

Defz * turn off trimming * turn off contig correction * use fewer kmers Mebbe * trim to 50x

Given that the overlapping PE belong in `--s-2` then perhaps it might be worth considering **not** ignoring the orphan R1 and R2 reads from the trimmomatic output (currently `/dev/null`) and...

Missing capability of "synteny" + "splitting paralogs" ?

3

We had recent bioinformatics group meeting and it became apparent that there may be some missing functionality in `roary` with respect to its use of synteny and its treatment of...

2.4.0 has nno configure script I had to still to `autoreconf -i -f`

Reason for pymummer<=0.10.3 ?

2

``` ERROR: ariba 2.13.5 has requirement pymummer