Overview Sequencing Summary Assembly Summary Repeat masking GeMoMa prediction MAKER prediction Non-coding RNA genes Functional Protein Classification Protein domain annotation Comparative Genomics DOGMA analysis BUSCO analysis

Description

This page was created to store the assembly data that was used for further analysis. There are two tables describing different types of sequence assemblies (genome assemblies and transcript assemblies). The Overview section describes the transcriptome construction.

Genome Data

Species	Download	Assembly level	Sequencing method	Material	Assembly Tool	Number of sequences	Nucleotides in sequences [nt]	Shortest sequence [nt]	Longest sequence [nt]	Median sequence length	Mean sequence length	N50 [nt]	NG50 [nt]	N90 [nt]	Percentage of N's	Total number of N's	GC-content	Sequence size distribution graph	Notes
Pogonomyrmex californicus	[Supernova 2.1 assembly] [Download fasta index]	Scaffold	10X Genomics	nuclear DNA	Supernova 2.1	6,793	241,082,378	460	1,993,378	5,353	35,489	208,871	1,993,378	16,229	1.15 %	3,132,150	36.3 %	[View part]	-
Pogonomyrmex californicus	[Supernova 2.0 assembly] [Download fasta index]	Scaffold	10X Genomics	nuclear DNA	Supernova 2.0	12,983	314,017,594	395	8,422,444	4,713	24,187	1,497,864	8,422,444	9,161	3.07 %	9,650,154	36.6 %	[View global] [View detailed]	-
Pogonomyrmex barbatus	-	Scaffold	454 XLR titanium platform at SeqWright	nuclear DNA	CABOG (v. 5.3)	4,645	235,645,958	297	3,918,663	1,353	50,731	819,605	3,918,663	117,988	6.6 %	15,575,506	34 %	[View global] [View detailed]	RefSeq assembly accession: GCF_000188075.1 NCBI ID: 243358
Camponotus floridanus	-	Scaffold	PacBio	nuclear DNA	canu (v. 1.3)	10,791	284,009,182	6,425	10,163,455	106,195	432,281	1,585,631	10,163,455	211,219	2.87 %	8,162,210	26 %	[View global] [View detailed]	RefSeq assembly accession: GCF_003227725.1 NCBI ID: 1752781
Solenopsis invicta (red fire ant)	-	Scaffold	454 Illumina	nuclear DNA	SOAPdenovo (v. 1.04) Newbler (v. 2.3)	69,511	396,024,718	200	6,355,204	721	5,967	558,018	6,355,204	12,516	0.13 %	538,573	25 %	[View global] [View detailed]	RefSeq assembly accession: GCF_000188075.1 NCBI ID: 244018 sex: male
Solenopsis invicta	-	Chromosome	454 Illumina	mitochondrial DNA	SOAPdenovo (v. 1.04) Newbler (v. 2.3)	1	15,549	-	-	-	-	-	-	-	0 %	0	22.83 %	-	RefSeq assembly accession: NC_014672.1
Apis mellifera (honey bee)	-	Chromosome	Sanger SOLiD 454	nuclear DNA	Atlas assembly system (v. before 2011)	5,321	250,287,000	540	29,893,408	1,351	47,037	13,219,345	29,893,408	147,519	0.11 %	276,584	21.67 %	[View global] [View detailed]	RefSeq assembly accession: GCF_000002195.4 NCBI ID: 254398

Transcriptome Data

Species	Download	Assembly level	Sequencing method	Source	Assembly Tool	Number of sequences	nucleotides in sequences [nt]	shortest sequence [nt]	longest sequence [nt]	Median sequence length	Mean sequence length	N50 [nt]	NG50 [nt]	N90 [nt]	percentage of N's	total number of N's	GC-content	Sequences size distribution graph	Notes
Pogonomyrmex californicus	[Downloaded from here]	transcript contigs	Illumina Hiseq 2000 [Done by M. Helmkampf et al. (2016)]	RNA from Head	Trinity (v. 1) [Done by M. Helmkampf et al. (2016)]	7,890	31,829,855	237	27,920	3,434	4,034	5,055	27,920	2,269	0 %	0	38.2 %	[View detailed] [View global] [View filtered global] [View filtered detailed]	This assembly was published by M. Helmkampf et al. (2016) , trimmed with Trim_galore v. 0.3.1 and filtered by FPKM of 0.14.
Pogonomyrmex californicus	[Download fasta] [Download gff]	transcript contigs	Illumina Hiseq 2000 [Done by M. Helmkampf et al. (2016)]	RNA from Head	Trinity (v. 2)	160,741	137,321,817	251	19,115	547	854	1,219	19,115	360	0 %	0	37.7 %	[View detailed] [View global] [View filtered global] [View filtered detailed]	Used published RNA raw reads. Trimmed with Trim_galore v. 0.5.0.
Pogonomyrmex californicus	[Download fasta] [Download gtf]	transcript contigs	Illumina Hiseq 2000 [Done by M. Helmkampf et al. (2016)]	RNA from Head	Tuxedo Suite (v. 1)	34,953	71,805,488	79	26,134	1,490	2,054	2,760	26,134	1,005	0.004 %	2,772	37 %	[View global] [View detailed]	Used published RNA raw reads. Trimmed with Trim_galore v. 0.5.0:
Pogonomyrmex californicus	[Download fasta] [Download gtf]	transcript contigs	Illumina Hiseq 2000 [Done by M. Helmkampf et al. (2016)]	RNA from Head	Tuxedo Suite (v. 2)	51441	107,364,332	200	30,234	1,513	2,087	3,163	30,234	1,033	0.002 %	2,741	37.64 %	[View global] [View detailed]	Used published RNA raw reads. Trimming with Trim_galore v. 0.5.0:
Pogonomyrmex californicus	[Download fasta] [Download gtf]	transcript contigs	MinION	RNA	-	10,700	12,715,775	200	31,833	991	1,188	1,450	31,833	648	0 %	0	35.49 %	[View global]	Stringtie (v. 2.0)
Pogonomyrmex californicus	[Download fasta] [Download gtf]	merged transcript assembly	Illumina and MinION	RNA	Stringtie (v. 2.0), Tuxedo Suite (v. 1 and v. 2) and Trinity (v. 1 and v. 2)	31,515	52,754,802	200	33,094	1,171	1,673	2,502	33,094	812	0.03 %	18,348	37.4 %	[View global] [View detailed]	Merged final transcript assembly (see Overview)

Discussion

Figure 1: Evaluation of the quality and completeness of genome assemblies from different species and assemblers. The P. californicus assemblies have been assembled
with Supernova v. 1, 2.0, and 2.1. The assembler Supernova (v. 2.1) includes the option of choosing a coverage. Assemblies with different genome coverage have been generated and evaluated.

Figure 2: Distribution of inter contig duplications within the Supernova 2.1 (75x) genome assembly.

Figure 3: Detailed Plot for displaying a higher resolution of duplicated sequences within the genome assemblies from Figure 1.

Figure 4: Genome assembly sequence length distribution. Based on the genome assembly which was generated by Supernova 2.1 with the sequencing depth of 75x.
The last bar in this graph displays all sequences which are longer than 40 kbp.

Figure 5: Detailed Plot for displaying duplicated sequences within the genome assemblies between contigs.