Question: How to plot length distribution of contigs in the assembly?
2
gravatar for seta
3.1 years ago by
seta1.0k
Sweden
seta1.0k wrote:

Dear all,

Could anybody please let me know if there is a convenient way to plot distribution of  contigs numbers vs. contig length?

Thanks

ADD COMMENTlink modified 2 days ago by Vijay Lakhujani3.1k • written 3.1 years ago by seta1.0k
1
gravatar for thackl
3.1 years ago by
thackl2.5k
European Union
thackl2.5k wrote:

Quast produces such plots and other useful assembly statistics as well. See also Quast Is A Convenient Tool For Assembly Evaluation.

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by thackl2.5k
0
gravatar for doctor.dee005
2 days ago by
doctor.dee005170
Bioinformatics Center, Pune
doctor.dee005170 wrote:

use this Python script. Easy to use: python contigPlot.py fastaDir.

Where fastaDir is directory name containing genome files (extension .fasta)

ADD COMMENTlink written 2 days ago by doctor.dee005170
0
gravatar for Vijay Lakhujani
2 days ago by
Vijay Lakhujani3.1k
India
Vijay Lakhujani3.1k wrote:

Check out a shell wrapper in the link below which is based on seqkit that I wrote couple of weeks ago

C: SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation in

ADD COMMENTlink modified 2 days ago • written 2 days ago by Vijay Lakhujani3.1k
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