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Merge branch 'flye' into flye-devel
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mikolmogorov committed Feb 19, 2018
2 parents cf51e75 + 36e0a91 commit ee8e5eb
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4 changes: 2 additions & 2 deletions docs/USAGE.md
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Expand Up @@ -64,7 +64,7 @@ The original dataset is available at the
[PacBio website](https://github.com/PacificBiosciences/DevNet/wiki/E.-coli-Bacterial-Assembly).
We coverted the raw ```bas.h5``` file to the FASTA format for the convenience.

wget https://github.com/fenderglass/datasets/raw/master/pacbio/E.coli_PacBio_40x.fasta
wget https://zenodo.org/record/1172816/files/E.coli_PacBio_40x.fasta
flye --pacbio-raw E.coli_PacBio_40x.fasta --out-dir out_pacbio --genome-size 5m --threads 4

with ```5m``` being the expected genome size, the threads argument being optional
Expand All @@ -76,7 +76,7 @@ where the assembly results will be placed.
The dataset was originally released by the
[Loman lab](http://lab.loman.net/2015/09/24/first-sqk-map-006-experiment/).

wget https://github.com/fenderglass/datasets/raw/master/ont/Loman_E.coli_MAP006-1_2D_50x.fasta
wget https://zenodo.org/record/1172816/files/Loman_E.coli_MAP006-1_2D_50x.fasta
flye --nano-raw Loman_E.coli_MAP006-1_2D_50x.fasta --out-dir out_nano --genome-size 5m --threads 4


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