R. sphaeroides

Rhodobacter sphaeroides strain 2.4.1. The R. sphaeroides 2.4.1 consists of two circular chromosomes of 3,188,609 bp and 943,016 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 illumina read data of R. sphaeroides were available at Gage-B.

Sequence assembly

We have downloaded scaffolding assemblies from SPAdes website.

Contig integrator

We have used CISA to integrate the assemblies and generated CISA's contigs.

Evaluation

Benchmark genome

R. sphaeroides 2.4.1

Evaluated by QUAST

QUAST (QUAST v2.1)

Running QUAST needs gene and sequence information. There are 4388 genes in total.

Score with QUAST: 　more detail.

Basic statistics	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	2	6	5	0	3	9	17	24
Misassembled contigs length	24651	135726	40523	0	24631	1180527	564277	*1850338*
Genome statistics
Genome fraction (%)	97.529	85.608	91.915	87.77	98.068	99.37	97.437	*99.474*
# genes	4030 + 275 part	3685 + 128 part	4036 + 38 part	3348 + 592 part	4046 + 307 part	4347 + 23 part	4068 + 265 part	*4358 + 19 part*
# mismatches per 100 kbp	4.83	10.51	12.48	3.22	5.98	5.82	13.11	*6.42*
# indels per 100 kbp	3.43	7.97	5.84	3.34	3.9	3.63	8.34	*3.69*
# N's per 100kbp	0	20.77	4.83	0	139.23	0	739.09	*3.68*

A dot plot (pdf) of CISA assembly against the reference genome.

A dot plot (pdf) of SPAdes assembly against the reference genome.