Question: What genome assembler to choose for an unpaired FASTQ data derived from a Birch chloroplast?
0
gravatar for oxfordsoccer
2.4 years ago by
oxfordsoccer10
oxfordsoccer10 wrote:

What genome assembler to choose for an unpaired FASTQ data derived from a Birch chloroplast?

And other tools for pre- and post-processing also

File type Conventional base calls Encoding Sanger / Illumina 1.9 (actually Ion Torrent data) Total Sequences 376768 Sequences flagged as poor quality 0 Sequence length 5-376 %GC 36

ADD COMMENTlink modified 2.4 years ago by Asaf8.0k • written 2.4 years ago by oxfordsoccer10

You may want to try tadpole.sh from BBMap suite. It does well with small genomes. See guide here.

ADD REPLYlink written 2.4 years ago by genomax85k

Careful with this user.

ADD REPLYlink written 2.4 years ago by Michael Dondrup47k
0
gravatar for Asaf
2.4 years ago by
Asaf8.0k
Israel
Asaf8.0k wrote:

I'll go with SPAdes, try it with and without --meta

ADD COMMENTlink written 2.4 years ago by Asaf8.0k
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