Reason for excessive relocation misassemblies

Question

[alhicks32188]

Hi, I'm a first time user of SPAdes and QUAST, and when I check the quality of my assembled contigs with QUAST, I seem to be getting excessive relocation misassemblies. Does anyone have any insights into possible reasons for this?

[GenoMax]

Can you provide some additional information about what sort of sequencing this is (technology/cycles)? How many reads did you have? What are the stats from SPAdes/QUAST.

[alhicks32188]

I apologize - this was Illumina Hiseq (I unfortunately don't have any information about the sequencing conditions). For this example sample, there were 4188562 paired end reads. Below is the report from QUAST (note that the local misassemblies are short relocations). Please let me know if I can provide further information or if you have any suggestions.

# contigs (>= 0 bp) 332

# contigs (>= 1000 bp) 82

# contigs (>= 5000 bp) 54

# contigs (>= 10000 bp) 45

# contigs (>= 25000 bp) 37

# contigs (>= 50000 bp) 30

Total length (>= 0 bp) 5309221

Total length (>= 1000 bp) 5241158

Total length (>= 5000 bp) 5187846

Total length (>= 10000 bp) 5119347

Total length (>= 25000 bp) 4989178

Total length (>= 50000 bp) 4694516

# contigs 97

Largest contig 662720

Total length 5251550

Reference length 5475491

GC (%) 69.03

Reference GC (%) 68.99

N50 177989

NG50 177989

N75 92868

NG75 90612

L50 10

LG50 10

L75 20

LG75 21

# misassemblies 59

# misassembled contigs 26

Misassembled contigs length 4029397

# local misassemblies 40

# unaligned contigs 27 + 24 part

Unaligned length 358784

Genome fraction (%) 84.636

Duplication ratio 1.056

# N's per 100 kbp 0.00

# mismatches per 100 kbp 854.01

# indels per 100 kbp 27.56

Largest alignment 254011

Total aligned length 4638230

NA50 71628

NGA50 70943

NA75 27975

NGA75 25368

LA50 21

LGA50 22

LA75 49

LGA75 56



misassemblies 59

# relocations 59

# translocations 0

# inversions 0

# misassembled contigs 26

Misassembled contigs length 4029397

# local misassemblies 40

# mismatches 39577

# indels 1277

# indels (<= 5 bp) 999

# indels (> 5 bp) 278

Indels length 7178

Misassemblies report

*All statistics are based on contigs of size >= 500 bp, unless otherwise noted (e.g., "# contigs (>= 0 bp)" and "Total length (>= 0 bp)" include all contigs).

Answer 1

[pcvgt]

I'm having this problem myself. Did you identify the source of the problem?