BasicAssemblyStats
From ArachneWiki
- For the more concise output module, see BasicStats.
| BasicAssemblyStats | |
|---|---|
| Function | Text output |
| Phase | Analysis |
| Standard CLAs | PRE, DATA, RUN, SUBDIR, GDB, NO_HEADER |
| Special CLAs | IGNORE_EMPTY_READS, UNGAPPED_STATS, SUPER_IDS, ARCHIVE |
| Source location | ARACHNE_DIR/reporting |
BasicAssemblyStats is a handy output module. It collects and prints a number of assembly statistics, including coverage, read usage, and contig and supercontig N50 values. It puts its output in a file called BasicAssemblyStats.out.
Output example
- Coverage. Note that sequence coverage assumes a genome of the size specified in genome.size, while assembly coverage assumes the genome size is equal to the assembly size.
Sequence coverage : 12.10 X Assembly coverage : 12.03 X
Sequence Q20 coverage : 10.21 X Assembly Q20 coverage : 10.21 X
- Read and base usage.
Number of reads in total : 120866 Number of reads used 0x : 8697 ( 7.2% ) Number of reads used 1x : 111930 ( 92.6% ) Number of reads used >1x : 239 ( 0.2% )
Number of bases in total : 84689085 Number of bases used 0x : 4781356 ( 5.6% ) Number of bases used 1x : 79721443 ( 94.1% ) Number of bases used >1x : 186286 ( 0.2% )
- Contig and (gapped/ungapped) supercontig lengths.
Contig N98 length : 6852 ( 78 large ones ) Contig N75 length : 83592 ( 28 large ones ) Contig N50 length : 164755 ( 14 Large ones ) Contig N25 length : 241825 ( 6 LARGE ones ) Contig total length : 6724648 ( 108 IN TOTAL )
Super N98 length : 9336 ( 6 large ones ) Super N75 length : 2880373 ( 2 large ones ) Super N50 length : 3585866 ( 1 Large ones ) Super N25 length : 3585866 ( 1 LARGE ones ) Super total length : 6641296 ( 29 IN TOTAL )
Ungap Super N98 length : 9336 ( 6 large ones ) Ungap Super N75 length : 2880373 ( 2 large ones ) Ungap Super N50 length : 3585866 ( 1 Large ones ) Ungap Super N25 length : 3585866 ( 1 LARGE ones ) Ungap Super total length : 6641296 ( 29 IN TOTAL )
- Statistics for contig coverage within supercontigs. Here ht is short for "height" -- i.e., the number of contigs piled onto a particular stretch. Positive-size gaps create regions of ht=0; negative-size gaps create regions of ht>1.
Region ht=0 N98 length : 194 ( 31 large ones ) Region ht=0 N75 length : 2725 ( 9 large ones ) Region ht=0 N50 length : 6092 ( 4 Large ones ) Region ht=0 N25 length : 8968 ( 2 LARGE ones ) Region ht=0 total length : 77540 ( 52 IN TOTAL )
Region ht=1 N98 length : 6677 ( 78 large ones ) Region ht=1 N75 length : 83314 ( 28 large ones ) Region ht=1 N50 length : 155843 ( 15 Large ones ) Region ht=1 N25 length : 234771 ( 6 LARGE ones ) Region ht=1 total length : 6402864 ( 108 IN TOTAL )
Region ht>1 N98 length : 1123 ( 6 large ones ) Region ht>1 N75 length : 26557 ( 2 large ones ) Region ht>1 N50 length : 106232 ( 1 Large ones ) Region ht>1 N25 length : 106232 ( 1 LARGE ones ) Region ht>1 total length : 160892 ( 27 IN TOTAL )
