BasicStats
From ArachneWiki
- For the more thorough output module, see BasicAssemblyStats.
| BasicStats | |
|---|---|
| Function | Text output |
| Phase | Analysis |
| Standard CLAs | PRE, DATA, RUN, SUBDIR, GDB, NO_HEADER |
| Special CLAs | OUTFILE, max_stretch, super_len_cutoff, suspect_links_file, BAD_LINKS, IGNORE_TINY, MAX_BASES_TO_IGNORE, QUAL_STATS, QUAL_STATS_ALT, FULL_QUAL_STATS, SMALLEST_SUPER_FOR_COVERAGE_STATS |
| Source location | ARACHNE_DIR/reporting |
BasicStats is a simple text output module that gives bare-bones information about an assembly. Its output looks like this (in this example, it was run with QUAL_STATS=True):
Supercontigs having < 3 reads or < 1kb sequence are ignored. 5 gaps <= -1000; 2 gaps <= -10000; 1 gaps <= -100000 fraction of gaps < -10kb or more than 4 deviations below zero: 10.1% 1 gaps > 10kb, 0 gaps > 50kb, 0 gaps > 200kb, 0 gaps > 1Mb 93.01% of reads were used in the assembly (94.35% of bases, 94.88% of Q20 bases) 0% of reads were used multiply in the assembly 108 contigs, having N50 length 164755 total contig length: 6724648, spanning 6803229 bases (with 1.16% in gaps) 29 supercontigs, having N50 length 3676149 (not including gaps) 2.57% of assembly in supers of size < 200000 (175057 bases) Assembly base coverage: 12.05X. Assembly Q20 coverage: 10.23X. 100% of bases have q >= 1 99.83% of bases have q >= 20 99.62% of bases have q >= 30 99.17% of bases have q >= 40 97.72% of bases have q >= 50
