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

Genomes are commonly stored as either fasta files (.fa) or twoBit (.2bit) files. Fasta files store the entire sequence as text and are thus not particularly compressed. twoBit files store each ...
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  • 880
25 votes

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

The standard formats for storing sequence data are fasta and fastq. Fasta is used if you only need the raw sequence data, fastq is used if you want to store the sequence data along with the quality ...
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  • 841
20 votes

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

The standard and the most common sequence format is FASTA for sure. You can compress it with a compressor. For the ~3GB human genome, gzip reduces the size to ~900MB, depending on the option in use. ...
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  • 5,764
13 votes

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

There are several things to consider when asking for "the most efficient" way to store data, it all depends on your use case. Do you just need ACGT, or are there also IUPAC codings for combinations? ...
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  • 744
13 votes
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The state, limitations and comparisons of large variant stores

An epic question. Unfortunately, the short answer is: no, there are no widely used solutions. For several thousand samples, BCF2, the binary representation of VCF, should work well. I don't see the ...
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12 votes
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Least present k-mers in the human genome

You can use the Jellyfish software to calculate the k-mer profiles up to length 31. From the instructions in the user guide: The basic command to count all k-mers is as follows: ...
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  • 2,566
11 votes

Downloading a reference Genome for Bowtie2

It’s a matter of preference I guess but I recommend the Ensembl builds. Decide whether you want the toplevel or primary assembly, and whether you want soft-masked, repeat-masked or unmasked files. The ...
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10 votes

Least present k-mers in the human genome

You can also use R. I give you an example of only chr1 and only kmer=4. ...
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  • 3,551
9 votes
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Downloading a reference Genome for Bowtie2

tl;dr: Just use the either the downloads on the Bowtie2 homepage or the Illumina iGenomes. Or just uncompress and concatenate the FASTA files found on UCSC goldenpath and then build the index. A bit ...
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  • 588
9 votes

Theoretical limit of human genome compression

For the most modern CHM13 assembly (v2.0; Complete T2T reconstruction of a human genome; https://github.com/marbl/CHM13), the best known compression without any use of a reference is 567 MB (1.45 bits/...
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8 votes
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How do I generate a variant list (i.e. VCF file) using Illumina reads from a human genome?

1. Adapter Trimming One of the first things I do after encountering a set of reads is to remove the adapter sequences from the start and end of reads. Most basecalling software includes some amount of ...
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8 votes
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Working with old genome builds

In my opinion, it is not very reliable. LiftOver is very limited in terms of transformations it can support. The LiftOver Chain format can capture only matching regions in the same order. It means ...
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8 votes

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

I think the question is a bit ambiguous so please excuse this answer that's a bit redundant from the rest of the ones provided. As others have mentioned, if you want to store a full genome, ...
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  • 181
7 votes

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

It is not yet standardized, but graph format has the potential for being the most space-efficient method for storing genomes. The idea is this: rather than store a genome as a linear string of ...
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  • 429
6 votes

What is the standard way to work with a diploid reference genome? Complementary strands?

At the moment, the standard reference genomes (e.g. hg19, hg38) are haploid genomes. We know that the human genome is diploid. Naturally, the latter would be the respectively correct representation of ...
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  • 2,086
6 votes

Retrieving a list of human genes having GO associations

I guess the following code will help, ...
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  • 584
6 votes

Retrieving a list of human genes having GO associations

Here's an example for the mouse genome: library(org.Mm.eg.db) select(org.Mm.eg.db, c("GO:0048406"), c("GENENAME","SYMBOL"), c("GO")) You get output like: ...
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6 votes
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Does the DNA or RNA of some ethnic groups map better than others' to the human reference genome sequence?

For simple variants like SNPs it would not really be a problem to use the current genome assembly for other ethnic groups. But for more complex variants this could be indeed problematic, however not ...
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  • 3,551
5 votes
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hg38 GTF file with RefSeq annotations

You will probably be interested in the following UCSC wiki page, which explains how to go from most of the UCSC tables to GTF/GFF: http://genomewiki.ucsc.edu/index.php/Genes_in_gtf_or_gff_format The ...
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5 votes

Using BLAT command line tool to blat split sequences

The FAQ offers an answer: I'm setting up my own Blat server and would like to use the same parameter values that the UCSC web-based Blat server uses. We almost always expect there to be some ...
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5 votes
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What is the standard way to work with a diploid reference genome? Complementary strands?

For calling small variants, the standard way is to simply call diploid genotypes. You can already do a variety of research with unphased genotypes. You may further phase genotypes with imputation, ...
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5 votes
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Dataset: Locations of regulatory sequences in the human genome?

This can be done quite easily using Ensebl's BioMart. Choose the Ensembl Regulation database: Select the "Human Regulatory Features" dataset: That's basically it right there, just click on "...
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  • 8,151
5 votes
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Authoritative source on human cytogenetic regions?

Do you mean cytoband coordinates? For the human genome you can find them for example at UCSC. hgdownload.cse.ucsc.edu/goldenPath/hg38/database/cytoBand.txt.gz
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  • 3,551
5 votes

Theoretical limit of human genome compression

There's a benchmark that compared dozens of compressors on DNA data, including human genome: http://kirr.dyndns.org/sequence-compression-benchmark/ In particular, this table shows file size of ...
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  • 51
4 votes

Working with old genome builds

I think that right now, the only human builds that are worth considering are hg19/GRCh37 as many data bases such as gnomAD still exclusively use this release. On the other hand, hg38/GRCh8 has many ...
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  • 588
4 votes

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

In terms of raw storage capacity 2 bits per nucleotide, and then further compressed with standard compression techniques would be the most efficient. However, you'd still have other storage ...
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4 votes

How do I generate a variant list (i.e. VCF file) using Illumina reads from a human genome?

The GATK is probably the most widely used program for this. There are several workflows you can use depending on what types of variants you're interested in (germline or somatic, short variants, copy ...
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4 votes

Least present k-mers in the human genome

Grabbing chromosomes for hg38: ...
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4 votes

What are the coordinates of the extended major histocompatibility complex (xMHC) in GRCh38?

Here is one definition of the classical MHC region: https://www.ncbi.nlm.nih.gov/grc/human/regions/MHC?asm=GRCh38.p13 which defines it as the 5mb region chr6:28510120-33480577 in GRCh38 coordinates. ...
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4 votes
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What does 'Human Alternative sequence Gene' mean in Ensembl?

These are genes on the patches and haplotypes. Patches are repairs in the genome, where they have discovered the sequence or assembly is incorrect, so there is an alternative sequence that is created ...
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