Retrieving assembly statistics for several accessions

Question

[genomes_and_MGEs]

Hey everyone,

I would like to download the global statistics for several assemblies. For example, on this link https://www.ncbi.nlm.nih.gov/assembly/GCF_000159415.1/, you can see the Global Statistics (sequence length, N50, number of contigs, etc.). I have a list of RefSeq accessions, like the one down:

GCF_000014425.1 GCF_000056065.1 GCF_000155915.2 GCF_000159335.1 GCF_000159355.1 GCF_000159415.1 GCF_000160855.1 GCF_000160875.1

Is it possible to extract Global Statistics for several RefSeq accessions? Probably using Entrez Direct. Cheers

Answer 1

[Pierre Lindenbaum]

using a XML transformation with xslt+xsltproc:

	<?xml version='1.0' encoding="UTF-8" ?>
	<xsl:stylesheet
	xmlns:xsl='http://www.w3.org/1999/XSL/Transform'
	xmlns:h='http://www.w3.org/1999/xhtml'
	version='1.0'>
	<xsl:output method="text"/>
	<xsl:template match="/">
	<xsl:apply-templates select="//h:table[@summary='Global statistics']/h:tbody/h:tr"/>
	</xsl:template>
	<xsl:template match="h:tr">
	<xsl:value-of select="substring-before(/h:html/h:head/h:title/text(),'- Genome')"/>
	<xsl:text> </xsl:text>
	<xsl:value-of select="h:td[1]/text()"/>
	<xsl:text> </xsl:text>
	<xsl:value-of select="h:td[2]/text()"/>
	<xsl:text>
	</xsl:text>
	</xsl:template>
	</xsl:stylesheet>

view raw biostars365290.xsl hosted with ❤ by GitHub

$ echo GCF_000014425.1 GCF_000056065.1 GCF_000155915.2 GCF_000159335.1 GCF_000159355.1 GCF_000159415.1 GCF_000160855.1 GCF_000160875.1 | tr " " "\n" |\
while read X; do wget -q -O -  "https://www.ncbi.nlm.nih.gov/assembly/${X}/"| xsltproc --novalid biostars365290.xsl - ; done

Output

ASM1442v1 	Total sequence length	1,894,360
ASM1442v1 	Total ungapped length	1,894,360
ASM1442v1 	Total number of chromosomes and plasmids	1
ASM5606v1 	Total sequence length	1,864,998
ASM5606v1 	Total ungapped length	1,864,998
ASM5606v1 	Total number of chromosomes and plasmids	1
Lacto_jensenii_1153_V2 	Total sequence length	1,746,219
Lacto_jensenii_1153_V2 	Total ungapped length	1,737,886
Lacto_jensenii_1153_V2 	Gaps between scaffolds	0
Lacto_jensenii_1153_V2 	Number of scaffolds	1
Lacto_jensenii_1153_V2 	Scaffold N50	1,746,219
Lacto_jensenii_1153_V2 	Scaffold L50	1
Lacto_jensenii_1153_V2 	Number of contigs	9
Lacto_jensenii_1153_V2 	Contig N50	903,202
Lacto_jensenii_1153_V2 	Contig L50	1
Lacto_jensenii_1153_V2 	Total number of chromosomes and plasmids	0
Lacto_jensenii_1153_V2 	Number of component sequences (WGS or clone)	9
ASM15933v1 	Total sequence length	1,604,632
ASM15933v1 	Total ungapped length	1,600,834
ASM15933v1 	Gaps between scaffolds	0
ASM15933v1 	Number of scaffolds	1
ASM15933v1 	Scaffold N50	1,604,632
ASM15933v1 	Scaffold L50	1
ASM15933v1 	Number of contigs	2
ASM15933v1 	Contig N50	832,947
ASM15933v1 	Contig L50	1
ASM15933v1 	Total number of chromosomes and plasmids	1
ASM15933v1 	Number of component sequences (WGS or clone)	2
ASM15935v1 	Total sequence length	1,780,499
ASM15935v1 	Total ungapped length	1,772,891
ASM15935v1 	Gaps between scaffolds	0
ASM15935v1 	Number of scaffolds	32
ASM15935v1 	Scaffold N50	1,030,662
ASM15935v1 	Scaffold L50	1
ASM15935v1 	Number of contigs	52
ASM15935v1 	Contig N50	139,200
ASM15935v1 	Contig L50	5
ASM15935v1 	Total number of chromosomes and plasmids	0
ASM15935v1 	Number of component sequences (WGS or clone)	52
ASM15941v1 	Total sequence length	2,248,406
ASM15941v1 	Total ungapped length	2,168,059
ASM15941v1 	Gaps between scaffolds	0
ASM15941v1 	Number of scaffolds	48
ASM15941v1 	Scaffold N50	475,421
ASM15941v1 	Scaffold L50	2
ASM15941v1 	Number of contigs	116
ASM15941v1 	Contig N50	44,004
ASM15941v1 	Contig L50	15
ASM15941v1 	Total number of chromosomes and plasmids	0
ASM15941v1 	Number of component sequences (WGS or clone)	116
ASM16085v1 	Total sequence length	2,020,582
ASM16085v1 	Total ungapped length	1,808,667
ASM16085v1 	Gaps between scaffolds	0
ASM16085v1 	Number of scaffolds	49
ASM16085v1 	Scaffold N50	288,743
ASM16085v1 	Scaffold L50	2
ASM16085v1 	Number of contigs	235
ASM16085v1 	Contig N50	15,586
ASM16085v1 	Contig L50	38
ASM16085v1 	Total number of chromosomes and plasmids	0
ASM16085v1 	Number of component sequences (WGS or clone)	235
ASM16087v1 	Total sequence length	1,277,649
ASM16087v1 	Total ungapped length	1,269,321
ASM16087v1 	Gaps between scaffolds	0
ASM16087v1 	Number of scaffolds	12
ASM16087v1 	Scaffold N50	246,521
ASM16087v1 	Scaffold L50	2
ASM16087v1 	Number of contigs	21
ASM16087v1 	Contig N50	246,521
ASM16087v1 	Contig L50	2
ASM16087v1 	Total number of chromosomes and plasmids	0
ASM16087v1 	Number of component sequences (WGS or clone)	22

view raw example.md hosted with ❤ by GitHub

[genomes_and_MGEs]

Thanks man! This is very helpful. I would like to show this data in a table. For example, first colum with descriptio, 2nd with sequence length, 3rd with no. of contigs, etc. Could you please let me know out to do that? Thanks!