What is the meaning of miniasm -2S6 command?

Question

[traditionalGuy]

I was trying to assemble oxford nanopore reads and was getting an empty gfa file as output. I found this solution https://github.com/lh3/miniasm/issues/18. And it worked ( it returned an non-empty gfa file). But i don't understand the command, miniasm usage doesn't have a -2S6 command. Here is what I get when I hit miniasm --h:

Usage: miniasm [options] <in.paf>
Options:
  Pre-selection:
    -R          prefilter clearly contained reads (2-pass required)
    -m INT      min match length [100]
    -i FLOAT    min identity [0.05]
    -s INT      min span [2000]
    -c INT      min coverage [3]
  Overlap:
    -o INT      min overlap [same as -s]
    -h INT      max over hang length [1000]
    -I FLOAT    min end-to-end match ratio [0.8]
  Layout:
    -g INT      max gap differences between reads for trans-reduction [1000]
    -d INT      max distance for bubble popping [50000]
    -e INT      small unitig threshold [4]
    -f FILE     read sequences []
    -n INT      rounds of short overlap removal [3]
    -r FLOAT[,FLOAT]
                max and min overlap drop ratio [0.7,0.5]
    -F FLOAT    aggressive overlap drop ratio in the end [0.8]
  Miscellaneous:
    -p STR      output information: bed, paf, sg or ug [ug]
    -b          both directions of an arc are present in input
    -1          skip 1-pass read selection
    -2          skip 2-pass read selection
    -V          print version number
See miniasm.1 for detailed description of the command-line options.

[Alish]

Did you ever find an explanation for this? I have a very similar experience... although I'm using gDNA as opposed to RNA (in the original post)

Answer 1

[bvm]

I know it's an old threads, but I found some (probably) relevant info in the source code: https://github.com/lh3/miniasm/blob/10f000dfdacb2006105a76dd4ba2e2e66d4886af/main.c

S6 means stage = 6 (L.50) --> the code is skipped between L.160 and L.188

2 means no_second (L.59) --> the code is skipped between L.128 and L.140