Question: What genome assembler to choose for an unpaired FASTQ data derived from a Birch chloroplast?
0
gravatar for oxfordsoccer
23 months 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 23 months ago by Asaf6.7k • written 23 months 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 23 months ago by genomax76k

Careful with this user.

ADD REPLYlink written 23 months ago by Michael Dondrup47k
0
gravatar for Asaf
23 months ago by
Asaf6.7k
Israel
Asaf6.7k wrote:

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

ADD COMMENTlink written 23 months ago by Asaf6.7k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 882 users visited in the last hour