source stringclasses 1
value | dedup_identity stringclasses 7
values | sample stringlengths 11 14 |
|---|---|---|
ATB_0.2.incr.202408 | 0.8 | SAMN13280448 |
ATB_0.2.incr.202408 | 0.8 | SAMEA5051014 |
ATB_0.2.incr.202408 | 0.8 | SAMN05216518 |
ATB_0.2.incr.202408 | 0.8 | SAMN16399251 |
ATB_0.2.incr.202408 | 0.8 | SAMN15375886 |
ATB_0.2.incr.202408 | 0.8 | SAMN04487775 |
ATB_0.2.incr.202408 | 0.8 | SAMN15366435 |
ATB_0.2.incr.202408 | 0.8 | SAMN40548968 |
ATB_0.2.incr.202408 | 0.8 | SAMEA104113837 |
ATB_0.2.incr.202408 | 0.8 | SAMEA3710311 |
ATB_0.2.incr.202408 | 0.8 | SAMN13173011 |
ATB_0.2.incr.202408 | 0.8 | SAMN04419115 |
ATB_0.2.incr.202408 | 0.8 | SAMN26511487 |
ATB_0.2.incr.202408 | 0.8 | SAMN02199229 |
ATB_0.2.incr.202408 | 0.8 | SAMN05421831 |
ATB_0.2.incr.202408 | 0.8 | SAMN05660860 |
ATB_0.2.incr.202408 | 0.8 | SAMEA111503894 |
ATB_0.2.incr.202408 | 0.8 | SAMN02440436 |
ATB_0.2.incr.202408 | 0.8 | SAMN08769589 |
ATB_0.2.incr.202408 | 0.8 | SAMN13350726 |
ATB_0.2.incr.202408 | 0.8 | SAMN14906828 |
ATB_0.2.incr.202408 | 0.8 | SAMN07572566 |
ATB_0.2.incr.202408 | 0.8 | SAMN29228794 |
ATB_0.2.incr.202408 | 0.8 | SAMN06454786 |
ATB_0.2.incr.202408 | 0.8 | SAMN06457300 |
ATB_0.2.incr.202408 | 0.8 | SAMN04488029 |
ATB_0.2.incr.202408 | 0.8 | SAMEA2203400 |
ATB_0.2.incr.202408 | 0.8 | SAMN10363430 |
ATB_0.2.incr.202408 | 0.8 | SAMN16288725 |
ATB_0.2.incr.202408 | 0.8 | SAMN36984869 |
ATB_0.2.incr.202408 | 0.8 | SAMN00809120 |
ATB_0.2.incr.202408 | 0.8 | SAMN02744040 |
ATB_0.2.incr.202408 | 0.8 | SAMN04488523 |
ATB_0.2.incr.202408 | 0.8 | SAMN05443507 |
ATB_0.2.incr.202408 | 0.8 | SAMN02441265 |
ATB_0.2.incr.202408 | 0.8 | SAMN07163071 |
ATB_0.2.incr.202408 | 0.8 | SAMN04488238 |
ATB_0.2.incr.202408 | 0.8 | SAMN07621946 |
ATB_0.2.incr.202408 | 0.8 | SAMN14590150 |
ATB_0.2.incr.202408 | 0.8 | SAMN20522874 |
ATB_0.2.incr.202408 | 0.8 | SAMN34073859 |
ATB_0.2.incr.202408 | 0.8 | SAMEA114036619 |
ATB_0.2.incr.202408 | 0.8 | SAMN28071806 |
ATB_0.2.incr.202408 | 0.8 | SAMEA5215814 |
ATB_0.2.incr.202408 | 0.8 | SAMN04488123 |
ATB_0.2.incr.202408 | 0.8 | SAMN02440920 |
ATB_0.2.incr.202408 | 0.8 | SAMN15871862 |
ATB_0.2.incr.202408 | 0.8 | SAMN02745130 |
ATB_0.2.incr.202408 | 0.8 | SAMN02194465 |
ATB_0.2.incr.202408 | 0.8 | SAMN02198961 |
ATB_0.2.incr.202408 | 0.8 | SAMN06266776 |
ATB_0.2.incr.202408 | 0.8 | SAMN14515634 |
ATB_0.2.incr.202408 | 0.8 | SAMN02441803 |
ATB_0.2.incr.202408 | 0.8 | SAMEA114266245 |
ATB_0.2.incr.202408 | 0.8 | SAMN31060702 |
ATB_0.2.incr.202408 | 0.8 | SAMN02910456 |
ATB_0.2.incr.202408 | 0.8 | SAMN08125777 |
ATB_0.2.incr.202408 | 0.8 | SAMN14908454 |
ATB_0.2.incr.202408 | 0.8 | SAMN02746064 |
ATB_0.2.incr.202408 | 0.8 | SAMN09064081 |
ATB_0.2.incr.202408 | 0.8 | SAMEA5613712 |
ATB_0.2.incr.202408 | 0.8 | SAMN07424629 |
ATB_0.2.incr.202408 | 0.8 | SAMN41724992 |
ATB_0.2.incr.202408 | 0.8 | SAMN06296520 |
ATB_0.2.incr.202408 | 0.8 | SAMN08886400 |
ATB_0.2.incr.202408 | 0.8 | SAMD00233765 |
ATB_0.2.incr.202408 | 0.8 | SAMN05421736 |
ATB_0.2.incr.202408 | 0.8 | SAMN10363436 |
ATB_0.2.incr.202408 | 0.8 | SAMN14395376 |
ATB_0.2.incr.202408 | 0.8 | SAMN02256494 |
ATB_0.2.incr.202408 | 0.8 | SAMN10363316 |
ATB_0.2.incr.202408 | 0.8 | SAMN38696006 |
ATB_0.2.incr.202408 | 0.8 | SAMN26232512 |
ATB_0.2.incr.202408 | 0.8 | SAMN07621123 |
ATB_0.2.incr.202408 | 0.8 | SAMN04488023 |
ATB_0.2.incr.202408 | 0.8 | SAMN03436211 |
ATB_0.2.incr.202408 | 0.8 | SAMEA8700209 |
ATB_0.2.incr.202408 | 0.8 | SAMN04489760 |
ATB_0.2.incr.202408 | 0.8 | SAMN05421820 |
ATB_0.2.incr.202408 | 0.8 | SAMD00064387 |
ATB_0.2.incr.202408 | 0.8 | SAMN02440755 |
ATB_0.2.incr.202408 | 0.8 | SAMN00103628 |
ATB_0.2.incr.202408 | 0.8 | SAMN28905067 |
ATB_0.2.incr.202408 | 0.8 | SAMN02261347 |
ATB_0.2.incr.202408 | 0.8 | SAMN12025133 |
ATB_0.2.incr.202408 | 0.8 | SAMN11029899 |
ATB_0.2.incr.202408 | 0.8 | SAMN12594299 |
ATB_0.2.incr.202408 | 0.8 | SAMN40207669 |
ATB_0.2.incr.202408 | 0.8 | SAMN14505994 |
ATB_0.2.incr.202408 | 0.8 | SAMN02261265 |
ATB_0.2.incr.202408 | 0.8 | SAMN00713572 |
ATB_0.2.incr.202408 | 0.8 | SAMEA3643042 |
ATB_0.2.incr.202408 | 0.8 | SAMN02745127 |
ATB_0.2.incr.202408 | 0.8 | SAMEA5613713 |
ATB_0.2.incr.202408 | 0.8 | SAMN04488695 |
ATB_0.2.incr.202408 | 0.8 | SAMN23166222 |
ATB_0.2.incr.202408 | 0.8 | SAMEA6124629 |
ATB_0.2.incr.202408 | 0.8 | SAMN02441051 |
ATB_0.2.incr.202408 | 0.8 | SAMN31060681 |
ATB_0.2.incr.202408 | 0.8 | SAMN08775545 |
End of preview. Expand in Data Studio
List of sample identifiers from ATB deduplicated at varying levels of identity based on nucleotide sequence using sketchlib v0.2.4.
Sketching and distance calculation conducted with below commands
sketchlib sketch -f ${infile} -o ${outpref} --k-vals 21 -s 10000 --threads 11
sketchlib dist ${outpref} -k 21 --ani --threads 11 -o ${outpref}_dists.tsv
Where infile is a set of genome inputs in the format:
GENOME000001 /path/to/GENOME000001.fasta
GENOME000002 /path/to/GENOME000002.fasta
GENOME000003 /path/to/GENOME000003.fasta
Representatives were then generated using the get_representatives.py script:
python get_representatives.py --infile ${outpref}_dists.tsv --min-return 1 --workflow reps_graph --threshold 0.80,0.85,0.90,0.95,0.98,0.99,1.0 --outpref ${outpref} --workflow reps
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