User: Nikolay Vyahhi
Nikolay Vyahhi • 1.1k
- Reputation:
- 1,070
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- Location:
- St. Petersburg, Russia
- Website:
- http://spbsu.ru/vyahhi
- Last seen:
- 8 months ago
- Joined:
- 6 years, 10 months ago
- Email:
- v*****@gmail.com
Working in Pavel Pevzner's Lab in St. Petersburg
Posts by Nikolay Vyahhi
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10
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... Commenting on my own old question: Rosalind is an online platform for learning bioinformatics through problem solving.
...
written 4.2 years ago by
Nikolay Vyahhi • 1.1k
19
votes
0
answers
4.8k
views
9 follow
0
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... QUAST is a convenient tool for assembly evaluation. QUAST paper has been accepted to Bioinformatics, and now it is available in Advanced Access.
QUAST computes a number of well-known metrics, including contig accuracy, number of genes discovered, N50, and others. It also introduces some new statist ...
written 4.6 years ago by
Nikolay Vyahhi • 1.1k
• updated
15 months ago by
Vijay Lakhujani • 1.2k
0
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8
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11k
views
8
answers
... QUAST paper was published in Bioinformatics — http://bioinformatics.oxfordjournals.org/content/early/2013/02/18/bioinformatics.btt086.abstract
...
written 4.6 years ago by
Nikolay Vyahhi • 1.1k
2
votes
6
answers
3.5k
views
6
answers
Answer:
A: How To Parse Fastq File?
... In Python:
for line in open('file.fastq'):
print line.replace('/1', '-1').replace('/2', '-2')
...
written 4.6 years ago by
Nikolay Vyahhi • 1.1k
1
vote
2
answers
1.5k
views
2
answers
... You can use GZIPInputStream to read gzipped files in Java.
More info here: http://www.javamex.com/tutorials/compression/gzip.shtml
...
written 4.7 years ago by
Nikolay Vyahhi • 1.1k
2
votes
4
answers
2.3k
views
4
answers
... To compare 2 species to determine how closely related they are, you can use SiBELia (Synteny Block ExpLoration tool) — it's able to compare bacterial genomes and visualize it in a useful way, see http://bioinf.spbau.ru/en/sibelia (description) or https://github.com/bioinf/Sibelia (code).
...
written 4.8 years ago by
Nikolay Vyahhi • 1.1k
1
vote
7
answers
2.5k
views
7
answers
... SiBELia (Synteny Block ExpLoration tool) is able to compare multiple bacterial genomes and visualize it in a useful way, see http://bioinf.spbau.ru/en/sibelia (description) or https://github.com/bioinf/Sibelia (code).
...
written 4.8 years ago by
Nikolay Vyahhi • 1.1k
2
votes
5
answers
5.7k
views
5
answers
... QUAST (QUality ASsesment Tool for Genome Assembly) can be used to assess the quality of genome assemblies (both de novo reference based):
http://bioinf.spbau.ru/quast
http://sourceforge.net/p/quast (code)
http://http://quast.bioinf.spbau.ru (QUAST server, beta)
...
written 4.8 years ago by
Nikolay Vyahhi • 1.1k
18
votes
8
answers
11k
views
8
answers
... QUAST (QUality ASsesment Tool for Genome Assembly) can be used to assess the quality of genome assemblies (both de novo reference based):
http://bioinf.spbau.ru/quast
http://sourceforge.net/p/quast (code)
http://quast.bioinf.spbau.ru (QUAST server, beta)
...
written 4.8 years ago by
Nikolay Vyahhi • 1.1k
2
votes
5
answers
5.7k
views
5
answers
Answer:
A: How To Get The Read Depth?
... AFAIK read depth for CNV is coverage for this region in alignment.
E.g. if you identified that there is no gene/region (deletion), then it's depth = 0.
E.g. if you identified 2 copies of the same region, then depth will be about twice as usual depth (given uniformity of coverage).
...
written 5.1 years ago by
Nikolay Vyahhi • 1.1k
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