summary.seqs
The summary.seqs command will summarize the quality of sequences in an unaligned or aligned fasta-formatted sequence file.
Default Setting
Fasta is the only required parameter:
mothur > summary.seqs(fasta=amazon.fasta)
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 422 422 0 4 1
2.5%-tile: 1 436 436 0 4 3
25%-tile: 1 507 507 1 5 25
Median: 1 530 530 3 5 50
75%-tile: 1 961 961 6 6 74
97.5%-tile: 1 973 973 15 8 96
Maximum: 1 978 978 20 9 98
Mean: 1 678.235 678.235 4.54082 5.44898
# of Seqs: 98
For this unaligned fasta file, we see that all of the sequences started at position 1 (they’re unaligned) and had between 422 and 978 bases in them. The median length was 530 bases. We can also see that more than 75% of the sequences had at least one ambiguous base in them and at least one had 20. The final column indicates the length of the longest homopolymer in each sequence - 95% of the sequences had a homopolymer length between 4 and 8 bases long.
An output file (e.g. amazon.fasta.summary) lists each of these parameters for each sequence. For example:
seqname start end nbases ambigs polymer numSeqs
U68589 1 943 943 10 5 1
U68590 1 497 497 0 6 1
U68591 1 930 930 1 4 1
...
So we see that sequence U68589 was 943 bases long, had 10 ambiguous bases in it and the longest homopolymer in the sequence was 5 bases long. The numSeqs column is 1 because no name file was provided so we assume this sequence is unique.
If we had instead analyzed an aligned sequence file such as the greengenes alignment database:
mothur > summary.seqs(fasta=core_set_aligned.imputed.fasta)
Start End NBases Ambigs Polymer NumSeqs
Minimum: 69 6849 1423 0 4 1
2.5%-tile: 97 6849 1469 0 5 124
25%-tile: 109 6849 1507 0 5 1235
Median: 109 6849 1524 0 6 2470
75%-tile: 109 6849 1538 0 6 3704
97.5%-tile: 109 6857 1563 3 8 4815
Maximum: 109 6885 1609 30 11 4938
Mean: 107.857 6849.47 1521.43 0.222155 5.67294
# of Seqs: 4938
Now we see that all of the sequences are at least 1,423 bases long, very few have any ambiguous bases and most sequences start by position 109 and end by position 6,849. These data can be useful for removing sequences that don’t overlap or that have features indicating poor quality using the screen.seqs command.
name
You can also use a name file with the summary.seqs command.
mothur > summary.seqs(fasta=stool.unique.fasta)
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 183 183 0 3 1
2.5%-tile: 1 242 242 0 4 507
25%-tile: 1 258 258 0 5 5061
Median: 1 267 267 0 5 10121
75%-tile: 1 274 274 0 5 15181
97.5%-tile: 1 287 287 0 6 19735
Maximum: 1 373 373 0 6 20241
Mean: 1 265.647 265.647 0 4.9541
# of Seqs: 20241
or
mothur > summary.seqs(fasta=stool.unique.fasta, name=stool.names)
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 183 183 0 3 1
2.5%-tile: 1 243 243 0 4 929
25%-tile: 1 259 259 0 5 9282
Median: 1 267 267 0 5 18564
75%-tile: 1 274 274 0 5 27845
97.5%-tile: 1 287 287 0 6 36198
Maximum: 1 373 373 0 6 37126
Mean: 1 265.768 265.768 0 4.96205
# of unique seqs: 20241
total # of seqs: 37126
count
The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence.
mothur > summary.seqs(fasta=stool.unique.fasta, count=stool.count_table)
summary && contigsreport && alignreport
The summary parameter allows you to provide a *.summary file as an input file.
mothur > summary.seqs(summary=stability.trim.contigs.good.unique.good.summary)
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1250 11550 250 0 3 1
2.5%-tile: 1968 11550 252 0 4 4711
25%-tile: 1968 11550 252 0 4 47109
Median: 1968 11550 252 0 4 94218
75%-tile: 1968 11550 253 0 5 141326
97.5%-tile: 1968 11550 253 0 6 183724
Maximum: 1968 13383 259 0 8 188434
Mean: 1967 11550 252 0 4
# of unique seqs: 20336
total # of seqs: 188434
The contigsreport parameter allows you to provide the *contigs.report file as input.
mothur > summary.seqs(contigsreport=stability.contigs.report)
Length Overlap_Length Overlap_Start Overlap_End MisMatches Num_Ns NumSeqs
Minimum: 246 0 0 83 0 0 1
2.5%-tile: 252 248 1 251 0 0 5699
25%-tile: 252 249 1 251 0 0 56989
Median: 252 249 2 251 2 0 113978
75%-tile: 253 250 2 251 7 0 170967
97.5%-tile: 253 250 3 252 31 7 222257
Maximum: 501 254 251 263 124 238 227955
Mean: 252 248 2 251 5 0
# of Seqs: 227955
The align report parameter allows you to provide an align.report file as input.
mothur > summary.seqs(alignreport=stability.MISeq_SOP.trim.contigs.good.unique.align.report)
Length SimBtwnQueryTemplate LongestInsert SearchScore NumSeqs
Minimum: 250 70 0 12 1
2.5%-tile: 252 86 0 48 411
25%-tile: 252 92 0 63 4107
Median: 253 94 0 71 8214
75%-tile: 253 97 0 87 12320
97.5%-tile: 254 99 0 96 16016
Maximum: 270 100 3 100 16426
Mean: 252 94 0 74
# of Seqs: 16426
processors
The processors option enables you to accelerate the summary process by using multiple processors. Default processors=Autodetect number of available processors and use all available. You can use 2 processors with the following option:
mothur > summary.seqs(fasta=stool.unique.fasta, name=stool.names, processors=2)
Revisions
- 1.22.0 - Added processors option for Windows users.
- 1.22.0 - Added NumSeqs and mean values to output.
- 1.28.0 - Added count option
- 1.31.0 - Bug Fix: 32bit machines processing a file larger than 4G could hang
- 1.39.1 - Adds file mismatch check
- 1.40.0 - Adds summary, contigsreport, alignreport parameters. #319
- 1.40.0 Rewrite of threaded code. Default processors=Autodetect number of available processors and use all available.
- 1.42.0 Removes extra space from output file names. #603