User: Nikolay Vyahhi

gravatar for Nikolay Vyahhi
Nikolay Vyahhi1.1k
Reputation:
1,070
Status:
Trusted
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

http://bioinf.spbau.ru/spades

Posts by Nikolay Vyahhi

<prev • 32 results • page 1 of 4 • next >
0
votes
10
answers
28k
views
10
answers
Comment: C: What Are The Best Bioinformatics Course Materials And Videos (Available Online)?
... Commenting on my own old question: Rosalind is an online platform for learning bioinformatics through problem solving. ...
written 4.2 years ago by Nikolay Vyahhi1.1k
19
votes
0
answers
4.8k
views
9 follow
0
answers
Tool: Quast Is A Convenient Tool For Assembly Evaluation
... 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 ...
assembly quality tool written 4.6 years ago by Nikolay Vyahhi1.1k • updated 15 months ago by Vijay Lakhujani1.2k
0
votes
8
answers
11k
views
8
answers
Comment: C: Assessing The Quality Of De Novo Assembled Data
... 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 Vyahhi1.1k
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 Vyahhi1.1k
1
vote
2
answers
1.5k
views
2
answers
Answer: A: How To Convert Pdb.Gz To Pdb Directly In In Java
... 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 Vyahhi1.1k
2
votes
4
answers
2.3k
views
4
answers
Answer: A: Closest Related Bacterial Species
... 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 Vyahhi1.1k
1
vote
7
answers
2.5k
views
7
answers
Answer: A: Comparative Microbial Genomics
... 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 Vyahhi1.1k
2
votes
5
answers
5.7k
views
5
answers
Answer: A: Soapdenovo Assembly Quality Assessment
... 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 Vyahhi1.1k
18
votes
8
answers
11k
views
8
answers
Answer: A: Assessing The Quality Of De Novo Assembled Data
... 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 Vyahhi1.1k
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 Vyahhi1.1k

Latest awards to Nikolay Vyahhi

Prophet 17 months ago, created a post with more than 20 followers. For What Are The Best Bioinformatics Course Materials And Videos (Available Online)?
Epic Question 2.9 years ago, created a question with more than 10,000 views. For What Are The Best Bioinformatics Course Materials And Videos (Available Online)?
Popular Question 2.9 years ago, created a question with more than 1,000 views. For What Is Nucmer'S "Percent Identity" Formally?
Good Answer 2.9 years ago, created an answer that was upvoted at least 5 times. For A: Project For A Beginner Bioinformatics Student
Student 2.9 years ago, asked a question with at least 3 up-votes. For What Are The Best Bioinformatics Course Materials And Videos (Available Online)?
Gold Standard 2.9 years ago, created a post with more than 25 bookmarks. For What Are The Best Bioinformatics Course Materials And Videos (Available Online)?
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Quast Is A Convenient Tool For Assembly Evaluation
Teacher 4.2 years ago, created an answer with at least 3 up-votes. For A: Open Reading Frame And Codons
Autobiographer 4.2 years ago, has more than 80 characters in the information field of the user's profile.
Appreciated 4.2 years ago, created a post with more than 5 votes. For A: Project For A Beginner Bioinformatics Student
Appreciated 4.2 years ago, created a post with more than 5 votes. For A: Open Reading Frame And Codons
Appreciated 4.2 years ago, created a post with more than 5 votes. For A: What Is Score Bits In Blast?
Appreciated 4.2 years ago, created a post with more than 5 votes. For A: Perl Program For Reading Fastq Format Files
Popular Question 4.2 years ago, created a question with more than 1,000 views. For What Are The Best Bioinformatics Course Materials And Videos (Available Online)?
Teacher 4.2 years ago, created an answer with at least 3 up-votes. For A: Project For A Beginner Bioinformatics Student
Guru 4.2 years ago, received more than 100 upvotes.
Voter 4.2 years ago, voted more than 100 times.
Supporter 4.2 years ago, voted at least 25 times.
Appreciated 4.6 years ago, created a post with more than 5 votes. For Quast Is A Convenient Tool For Assembly Evaluation
Good Answer 4.8 years ago, created an answer that was upvoted at least 5 times. For A: Assessing The Quality Of De Novo Assembled Data
Good Answer 5.1 years ago, created an answer that was upvoted at least 5 times. For A: Project For A Beginner Bioinformatics Student
Good Answer 5.6 years ago, created an answer that was upvoted at least 5 times. For A: Open Reading Frame And Codons
Teacher 5.6 years ago, created an answer with at least 3 up-votes. For A: Open Reading Frame And Codons
Teacher 6.0 years ago, created an answer with at least 3 up-votes. For A: What Is Score Bits In Blast?
Teacher 6.1 years ago, created an answer with at least 3 up-votes. For A: Perl Program For Reading Fastq Format Files

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 508 users visited in the last hour