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Old 03-22-2014, 10:44 AM   #1
morning latte
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Location: MI

Join Date: Jun 2013
Posts: 91
Default Help with interpreting IDBA_UD assembly output

Hello,

I was trying the IDBA_UD assembler for my metagenomes for the first time. I have been trying to find a documentation on interpreting the outputs but haven't found any. Could anyone help me with the output? I also went through old postings here but was not able to find the answer for my question. Any advice would be greatly appreciated!

An output directory containing multiple fasta files was generated after running the IDBA_UD. I assume that I have to use "contig.fa" for the further analysis. Am I correct? Could you explain differences between them?

I have hard time to interpret the "log" file. Below is the one I got. Which one is the stats for the final "contig.fa"? Why are there two "kmer of 60"?

number of threads 1
reads 46326304
long reads 0
extra reads 0
read_length 100
kmer 60
kmers 77958510 76121085
merge bubble 1215
contigs: 75437 n50: 119 max: 5289 mean: 118 total length: 8910129 n80: 63
aligned 1835482 reads
confirmed bases: 2768028 correct reads: 410078 bases: 343009
kmer 20
kmers 209804973 209944022
merge bubble 142969
contigs: 1324264 n50: 72 max: 6189 mean: 51 total length: 68617304 n80: 28
aligned 936011 reads
confirmed bases: 5037462 correct reads: 159618 bases: 20497
distance mean 271.123 sd 122.238
seed contigs 51438 local contigs 2648528
kmer 40
kmers 87229157 87354041
merge bubble 9179
contigs: 283618 n50: 261 max: 8023 mean: 127 total length: 36149932 n80: 71
aligned 1622279 reads
confirmed bases: 8349992 correct reads: 299441 bases: 27070
distance mean 280.19 sd 148.882
seed contigs 53979 local contigs 567236
kmer 60
kmers 52067154 52217769
merge bubble 2684
contigs: 136775 n50: 361 max: 12385 mean: 212 total length: 29072718 n80: 118
aligned 3012828 reads
confirmed bases: 9798172 correct reads: 417627 bases: 31962
distance mean 281.18 sd 147.978
seed contigs 47029 local contigs 273550
kmer 80
kmers 33745199 33462753
merge bubble 1343
contigs: 69296 n50: 478 max: 8256 mean: 343 total length: 23776057 n80: 301
aligned 9589068 reads
confirmed bases: 10063129 correct reads: 620205 bases: 192024
distance mean 261.349 sd 149.598
seed contigs 39512 local contigs 138592
kmer 100
kmers 20137243 19250177
merge bubble 959
contigs: 34622 n50: 594 max: 10832 mean: 569 total length: 19702800 n80: 377
reads 46326304
aligned 5056106 reads
distance mean 271.986 sd 147.421
expected coverage 0.310699
edgs 137
contigs: 34555 n50: 593 max: 16184 mean: 569 total length: 19690114 n80: 377
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Old 09-17-2014, 11:51 PM   #2
francicco
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Location: Innsbruck

Join Date: Jul 2010
Posts: 28
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I have se same question!
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