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user172818
  • Member for 5 years, 1 month
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24 votes
Accepted

What is the fastest way to calculate the number of unknown nucleotides in FASTA / FASTQ files?

20 votes

What's the most efficient file format for the storage of DNA sequences?

14 votes
Accepted

Meaning of BWA-MEM MAPQ scores

13 votes
Accepted

The state, limitations and comparisons of large variant stores

10 votes
Accepted

Single-sample vs. joint genotyping

10 votes

What is indel calling and what is its purpose?

9 votes
Accepted

What are the de facto required fields in a SAM/BAM read group?

9 votes

Are there any rolling hash functions that can hash a DNA sequence and its reverse complement to the same value?

9 votes

Library for computing BWT-based alignments

9 votes
Accepted

What Ensembl genome version should I use for alignments? (e.g. toplevel.fa vs. primary_assembly.fa)

8 votes

Accuracy of the original human DNA datasets sequenced by Human Genome Project?

8 votes
Accepted

How do kmer counters determine which kmer is 'canonical'?

8 votes
Accepted

Why Ti/Tv ratio?

8 votes

How to get fasta alignment file from SAM/BAM file?

8 votes

Are variant calling files personally identifiable information?

7 votes
Accepted

How should the popular press compare similarity of genomes?

7 votes
Accepted

How to write a hash function for canonical kmers?

7 votes

How do PCR duplicates arise and why is it important to remove them for NGS analysis?

7 votes
Accepted

How can I improve a long-read assembly with a repetitive genome?

7 votes

Rule Extraction from nnet results

7 votes

Why sequence the human genome at 30x coverage?

6 votes

Is there a way to retrieve several SAM fields faster than `samtools view | cut -f`?

6 votes

What's the best way to download data from the SRA? Is it really this slow?

6 votes
Accepted

Do variant calls change when you call from CRAM?

6 votes

How to calculate the memory usage of storing kmers in RAM

6 votes
Accepted

Why does cutadapt remove low quality bases from the ends of reads only?

6 votes

Counting repeated kmers sequences that match at least x % of reads sequence

6 votes

Remove/delete sequences by ID from multifasta

6 votes
Accepted

Is there a standard definition for "assembly polishing"?

6 votes

Are these standard species abbreviations and how to look up others?