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Question: How to analyze/Visualize the SPAdes result.
2
gravatar for roopashreekadaba97
13 months ago by
roopashreekadaba97 • 20
roopashreekadaba97 • 20 wrote:

Please can anyone help me to visualize and analyze the SPAdes result?===== Assembling finished. Used k-mer sizes: 21, 33, 55, 77

  • Corrected reads are in /home/pc30/SPAdes/roopa/corrected/
  • Assembled contigs are in /home/pc30/SPAdes/roopa/contigs.fasta
  • Assembled scaffolds are in /home/pc30/SPAdes/roopa/scaffolds.fasta
  • Assembly graph is in /home/pc30/SPAdes/roopa/assembly_graph.fastg
  • Assembly graph in GFA format is in /home/pc30/SPAdes/roopa/assembly_graph_with_scaffolds.gfa
  • Paths in the assembly graph corresponding to the contigs are in /home/pc30/SPAdes/roopa/contigs.paths
  • Paths in the assembly graph corresponding to the scaffolds are in /home/pc30/SPAdes/roopa/scaffolds.paths

======= SPAdes pipeline finished.

I got this in the terminal. But where do i get the total number of contigs, scaffolds count and all?
next-gen • 1.4k views
ADD COMMENT • link •
modified 13 months ago by Sej Modha ♦ 4.1k • written 13 months ago by roopashreekadaba97 • 20
2
gravatar for Sej Modha
13 months ago by
Sej Modha ♦ 4.1k
Glasgow, UK
Sej Modha ♦ 4.1k wrote:

You can visualise the assembly (.fastag) file using Bandage tool or you could use QUAST to look at the assembly stats.

ADD COMMENT • link written 13 months ago by Sej Modha ♦ 4.1k

This is a link to a perl script for getting assembly statistics https://raw.githubusercontent.com/KorfLab/Assemblathon/master/assemblathon_stats.pl

I have tested it on perl-5.10, but there are problems running it on perl-5.22.1

ADD REPLY • link written 13 months ago by jean.elbers • 740
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