User: Nikolay Vyahhi
Nikolay Vyahhi • 1.3k
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- St. Petersburg, Russia
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- http://spbsu.ru/vyahhi
- Last seen:
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- Joined:
- 9 years, 9 months ago
- Email:
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Working in Pavel Pevzner's Lab in St. Petersburg
Posts by Nikolay Vyahhi
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... Commenting on my own old question: Rosalind is an online platform for learning bioinformatics through problem solving.
...
written 7.1 years ago by
Nikolay Vyahhi • 1.3k
27
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7.7k
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17 follow
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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 7.5 years ago by
Nikolay Vyahhi • 1.3k
• updated
4.1 years ago by
lakhujanivijay ♦ 5.1k
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... QUAST paper was published in Bioinformatics — http://bioinformatics.oxfordjournals.org/content/early/2013/02/18/bioinformatics.btt086.abstract
...
written 7.5 years ago by
Nikolay Vyahhi • 1.3k
2
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6
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5.1k
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6
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Answer:
A: How To Parse Fastq File?
... In Python:
for line in open('file.fastq'):
print line.replace('/1', '-1').replace('/2', '-2')
...
written 7.5 years ago by
Nikolay Vyahhi • 1.3k
1
vote
2
answers
2.4k
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 7.6 years ago by
Nikolay Vyahhi • 1.3k
3
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4
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3.8k
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 7.7 years ago by
Nikolay Vyahhi • 1.3k
1
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7
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3.7k
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7
answers
... SiBELia (Synteny Block ExpLoration tool) is able to compare multiple bacterial genomes and visualize it in a useful way, see [description][1] or [code][2].
[1]: http://bioinf.spbau.ru/en/sibelia
[2]: https://github.com/bioinf/Sibelia ...
written 7.7 years ago by
Nikolay Vyahhi • 1.3k
• updated
18 months ago by
RamRS ♦ 28k
2
votes
5
answers
7.2k
views
5
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... 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 7.7 years ago by
Nikolay Vyahhi • 1.3k
20
votes
10
answers
17k
views
10
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 7.7 years ago by
Nikolay Vyahhi • 1.3k
2
votes
5
answers
10k
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 8.0 years ago by
Nikolay Vyahhi • 1.3k
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