Torsten Seemann

``` if ($in_seq) { # 421 ctctcaaact aaagccgtct cactctccat gagtcgttcg acagatcgcg ttttaaattg my $s = substr $_, 10; # trim the coordinate prefix $s =~ s/\s//g; $dna .= $s ....

Add `--outfmt bed` ? Perhaps if symlinked to `any2bed` it with `--outfmt bed` ? Useful for making `--mask` files for snippy etc

Maybe we want to parse NCBI pipe specifiers? eg `>gb|xxxxx|ref|yyyyyy|`

Default should be 60

``` >tig00008674 len=10963 reads=1 covStat=0.00 gappedBases=no class=contig suggestRepeat=no suggestCircular=no ```

Currently uses 1 .. N which is cleanand will always work, but names might be better.

Get file from circlator?

``` minimap2 -x sr ../db/NCBI bac/Salmonella_enterica_serovar_Typhimurium_T000240_uid84397/*fna [ERROR] incorrect input: in the sr mode, please specify no more than two query files. ```

If there is a tie, each are valid but we only print top one.

``` brew install brewsci/bio/repaq ```