What is the meaning of miniasm -2S6 command?
0
1
Entering edit mode
14 months ago

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.*
Assembly assembly oxford-nanopore miniasm • 425 views
ADD COMMENT
0
Entering edit mode

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)

ADD REPLY

Login before adding your answer.

Traffic: 1920 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6