We used Dataset 3, Streptococcus pneumoniae TIGR4
spades.py --pe1-1 frag_1.fastq --pe1-2 frag_2.fastq --mp1-1 jump_1.fastq --mp1-2 jump_2.fastq --pacbio long.fasta
spades.py --pe1-1 frag_1.fastq --pe1-2 frag_2.fastq --mp1-1 jump_1.fastq --mp1-2 jump_2.fastq
Basic statistics | Website Data | Raw Data |
# contigs | 20 | 90 |
Largest contig | 433183 | 423414 |
Total length | 2157030 | 2239813 |
N50 | 210016 | 365564 |
Misassemblies | ||
# misassemblies | 13 | 8 |
Misassembled contigs length | 1358992 | 815978 |
Mismatches | ||
# mismatches per 100kbp | 26.66 | 31.5 |
# indels per 100kbp | 4.52 | 2.89 |
# N's per 100kbp | 727.2 | 414.9 |
Genome statistics | ||
Genome fraction (%) | 98.267 | 99.177 |
Duplication ratio | 1.017 | 1.018 |
# genes | 2244 + 25 part | 2269 + 21 part |
NGA50 | 124123 | 208537 |
Running Time | 19m | 1hr 8m |
Misassemblies for Adobe reader.
Basic statistics | Website Data | Raw Data |
# contigs | 65 | 142 |
Largest contig | 247182 | 362472 |
Total length | 2176172 | 2192447 |
N50 | 84287 | 81903 |
Misassemblies | ||
# misassemblies | 19 | 3 |
Misassembled contigs length | 1114155 | 85063 |
Mismatches | ||
# mismatches per 100kbp | 20.9|18.33 | |
# indels per 100kbp | 2.14 | 2.1 |
# N's per 100kbp | 1305.04 | 1019.23 |
Genome statistics | ||
Genome fraction (%) | 97.185 | 97.179 |
Duplication ratio | 1.022 | 1.019 |
# genes | 2177 + 57 part | 2170 + 62 part |
NGA50 | 71450 | 81058 |
Running Time | 11m | 51m |
Misassemblies for Adobe reader.