How to analyze/Visualize the SPAdes result.

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

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updated 8.5 years ago by Sej Modha

• written 8.5 years ago by roopashreekadaba97 •

1 answer

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

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written 8.5 years ago by Sej Modha

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

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written 8.5 years ago by jean.elbers

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