could I get a script that can generate some basic statistics from the velvet output file (contigs.fa)
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Thanks. to be more specific I would like to see the following statistics for velvet output fasta file:
-Statistics for contig lengths:
Min contig length
Max contig length
Mean contig length
standard deviation of contig length
Median contig length
N50 contig length
- Statistics for no. of contigs:
No. of contigs
No of contigs >=1kb
No. of contigs in N50
-Statistics for bases in the contigs:
No. of bases in all contigs
No. of bases in contigs >=1kb
GC content of contigs
-Simple Dinucleotide repeats:
No. of contigs with over 70% dinucleotide repeats
AT
CG
AC
TG
AG
TC
_Simple mononucleotide repeats:
No. of contigs with over 50% dinucleotide repeats
AA
TT
CC
GG
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i don't which of your interest will be covered but have a look here velet std summary. I find the way they do it quite neat. However, i think you have to script something yourself to get all desired information.
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Using Biopieces (www.biopieces.org):
Assembled contigs can be analyzed to get some stats using analyze_assembly. We include a filtering step to discard contigs shorter than 200 bases:
Code:read_fasta -i contigs.fna | grab -e "SEQ_LEN>=200" | analyze_assembly -x
Code:N50: 9082 MAX: 52038 MIN: 200 MEAN: 4170 TOTAL: 3057214 COUNT: 733 ---
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