- For the more thorough output module, see BasicAssemblyStats.
|| Text output
| 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
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