MultiQC Analysis of 2016-07-01 MiSeq Trimmomatic trimmed data


MultiQC: a new program which summarises and contracts all the FastQC reports (given below)

FastQC Analysis of 2016-07-01 MiSeq Trommomatic trimmed data

500005_forward_paired_ | 500005_reverse_paired_
500024_forward_paired_ | 500024_reverse_paired_
500519_forward_paired_ | 500519_reverse_paired_
500523_forward_paired_ | 500523_reverse_paired_
501725_forward_paired_ | 501725_reverse_paired_
502749_forward_paired_ | 502749_reverse_paired_
502836_forward_paired_ | 502836_reverse_paired_
503710_forward_paired_ | 503710_reverse_paired_
504302_forward_paired_ | 504302_reverse_paired_
504782_forward_paired_ | 504782_reverse_paired_
505137_forward_paired_ | 505137_reverse_paired_
505907_forward_paired_ | 505907_reverse_paired_
506683_forward_paired_ | 506683_reverse_paired_
506776_forward_paired_ | 506776_reverse_paired_
606111_forward_paired_ | 606111_reverse_paired_
607239_forward_paired_ | 607239_reverse_paired_
BS20102N_forward_paired_ | BS20102N_reverse_paired_
MU572163T_forward_paired_ | MU572163T_reverse_paired_
Undetermined_forward_paired_ | Undetermined_reverse_paired_

SPAdes assembly statistics

filename total_length number mean_length longest shortest N_count Gaps N50 N50n N70 N70n N90 N90n
500005_trimmoed2/scaffolds.fasta 4,415,496 532 8299.80 202,281 49 0 0 37,651 35 24,339 64 8,112 119
500024_trimmoed2/scaffolds.fasta 5,044,256 2,368 2130.18 87,040 50 596 8 17,571 79 9,044 153 421 868
500519_trimmoed2/scaffolds.fasta 4,462,494 646 6907.89 204,855 78 561 9 37,915 35 22,820 64 8,333 123
500523_trimmoed2/scaffolds.fasta 5,798,186 3,406 1702.34 102,784 59 55 3 30,286 58 7,597 126 418 1,745
501725_trimmoed2/scaffolds.fasta 4,998,613 324 15427.82 352,348 78 632 10 121,642 13 66,458 24 28,243 44
502749_trimmoed2/scaffolds.fasta 4,806,900 1,478 3252.30 141,778 73 157 5 37,477 38 21,412 71 724 232
502836_trimmoed2/scaffolds.fasta 4,605,518 969 4752.86 138,615 78 243 8 42,468 34 25,928 61 5,530 125
503710_trimmoed2/scaffolds.fasta 4,496,643 793 5670.42 125,692 78 203 14 37,598 40 21,431 72 6,251 140
504302_trimmoed2/scaffolds.fasta 8,998,344 8,931 1007.54 120,805 78 786 37 1,451 300 601 2,480 385 6,322
504782_trimmoed2/scaffolds.fasta 5,815,744 3,137 1853.92 171,622 78 354 17 27,650 54 8,510 121 443 1,544
505137_trimmoed2/scaffolds.fasta 9,927,584 6,002 1654.05 149,215 78 2,767 234 2,718 886 1,489 1,885 667 3,832
Error opening file 505907_trimmoed2/scaffolds.fasta
506683_trimmoed2/scaffolds.fasta 4,408,644 671 6570.26 108,149 78 1,032 28 24,635 51 15,519 97 6,049 182
506776_trimmoed2/scaffolds.fasta 4,422,095 491 9006.30 195,158 78 285 5 42,259 31 29,887 56 11,080 102
606111_trimmoed2/scaffolds.fasta 4,606,577 1,077 4277.23 142,169 78 136 10 35,602 41 21,381 74 3,686 160
607239_trimmoed2/scaffolds.fasta 4,436,407 551 8051.56 217,149 78 130 2 52,934 31 32,982 53 11,967 98
BS20102N_trimmoed2/scaffolds.fasta 1,848,845 103 17949.95 336,201 78 0 0 209,973 4 115,362 6 66,842 10
MU572163T_trimmoed2/scaffolds.fasta 2,937,150 344 8538.23 125,565 78 228 4 25,659 32 17,471 59 5,500 114
Undetermined_trimmoed2/scaffolds.fasta 5,063,890 6,703 755.47 8,575 78 141 11 949 1,364 538 2,805 371 5,156