BasicAssemblyStats

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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

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   )
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