Question: How to analyze/Visualize the SPAdes result.
2
gravatar for roopashreekadaba97
22 months ago by
roopashreekadaba9720 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 • 2.4k views
ADD COMMENTlink modified 22 months ago by Sej Modha4.5k • written 22 months ago by roopashreekadaba9720
2
gravatar for Sej Modha
22 months ago by
Sej Modha4.5k
Glasgow, UK
Sej Modha4.5k wrote:

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

ADD COMMENTlink written 22 months ago by Sej Modha4.5k

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 REPLYlink written 22 months ago by jean.elbers1.3k
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: 1930 users visited in the last hour