script to get basic statistics from velvet contigs.fa

mmmm · 12-10-2013, 05:19 AM

could I get a script that can generate some basic statistics from the velvet output file (contigs.fa)

sphil · 12-10-2013, 05:30 AM

Please be more specific about what you need and what your understanding of "statistics from the velvet output" is. Do you mean N50, number of Contigs, longest, shortest....

mmmm · 12-10-2013, 05:52 AM

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

GenoMax · 12-10-2013, 06:02 AM

Take your pick:

https://github.com/ajmazurie/velvet-stats

http://milkweedgenome.org/?q=node/73

http://korflab.ucdavis.edu/datasets/...athon_stats.pl

sphil · 12-10-2013, 06:03 AM

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.

maasha · 12-11-2013, 01:10 AM

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

And the output:

Code:

N50: 9082
MAX: 52038
MIN: 200
MEAN: 4170
TOTAL: 3057214
COUNT: 733
---

There are many other options for stats as well. Look here:

https://code.google.com/p/biopieces/...aning_NGS_data

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12-10-2013, 05:19 AM	#1
mmmm Senior Member Location: UK Join Date: Jul 2013 Posts: 131	script to get basic statistics from velvet contigs.fa could I get a script that can generate some basic statistics from the velvet output file (contigs.fa)

12-11-2013, 01:10 AM	#6
maasha Senior Member Location: Denmark Join Date: Apr 2009 Posts: 153	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 And the output: Code: N50: 9082 MAX: 52038 MIN: 200 MEAN: 4170 TOTAL: 3057214 COUNT: 733 --- There are many other options for stats as well. Look here: https://code.google.com/p/biopieces/...aning_NGS_data

12-10-2013, 05:30 AM	#2
sphil Senior Member Location: Stuttgart, Germany Join Date: Apr 2010 Posts: 192	Please be more specific about what you need and what your understanding of "statistics from the velvet output" is. Do you mean N50, number of Contigs, longest, shortest....

12-10-2013, 05:52 AM	#3
mmmm Senior Member Location: UK Join Date: Jul 2013 Posts: 131	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

12-10-2013, 06:02 AM	#4
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,082	Take your pick: https://github.com/ajmazurie/velvet-stats http://milkweedgenome.org/?q=node/73 http://korflab.ucdavis.edu/datasets/...athon_stats.pl

12-10-2013, 06:03 AM	#5
sphil Senior Member Location: Stuttgart, Germany Join Date: Apr 2010 Posts: 192	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.