R. sphaeroides

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Rhodobacter sphaeroides strain 2.4.1. The R. sphaeroides 2.4.1 consists of a circular chromosome of 3,188,609 bp and five plasmids of 114,045 bp, 114,178 bp, 105,284 bp, 100,828 bp and 37,100 bp in length, respectively.

1 Read source
2 Sequence assembly
3 Contig integrator
4 Evaluation

Read source

The paired-end illuminia read data of R. sphaeroides were downloaded from Gage-B

Sequence assembly

There are eight assemblers, ABySS, CABOG, MaSuRCA, MIRA, SGA, SOAPdenovo, SPAdes 2.5 and Velvet, used in the data, and the scaffolding results were downloaded from SPAdes website

Contig integrator

Contigs

Evaluation

Benchmark genome

R. sphaeroides 2.4.1

Evaluated by QUAST

QUAST (QUAST v2.1)

Running QUAST needs gene and sequence information.

Score with QUAST: 　more detail

Basic statisitcs	ABySS	CABOD	MaSuRCA	SGA	SOAPdenovo	SPAdes 2.5	Velvet	CISA
# contigs	382	131	52	733	185	40	143	35
Largest contig	71578	177098	241348	44874	204500	739647	236829	*740054*
Total length	4503182	3953489	4247061	4091078	4549335	4781613	4526809	*4950301*
NG50	21441	40287	144812	7971	45133	518052	85272	*523557*
Misassemblies
# misassemblies	4	15	15	3	1	3	9	11
Misassembled contigs length	155883	1987058	765654	24763	90965	94799	723259	*2399227*
Genome statistics
Genome fraction (%)	98.444	99.334	99.009	97.438	98.099	98.554	97523	*99.38*
# genes	5819 + 64 part	5965 + 34 part	5964 + 34 part	5635 + 231 part	5839 + 44 part	5950 + 27 part	5604 + 275 part	*5980 + 28 part*
# mismatches per 100 kbp	6.62	4.43	8.96	0.7	8.16	2.07	5.93	6.08'
# indels per 100 kbp	7.57	5.86	5.95	2	5.69	2.39	30.28	*2.78*
# N's per 100kbp	116.43	17.43	7.49	0	8.51	15.24	783.91	*0.04*