Code

Minimap remove noise#102

Code

Merged

martinghunt merged 22 commits intosanger-pathogens:mastersanger-pathogens/ariba:masterfrom martinghunt:minimap_remove_noisemartinghunt/ariba:minimap_remove_noiseCopy head branch name to clipboardJul 19, 2016

+1,493-137

Commits

Commits on Jul 19, 2016

• Add cd-hit-est-2d

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  c91138e

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• Add fasta option

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  36a7fa6

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• Option to write interleaved file

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  b7fd74d

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• Test fasta interleaved

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  740511c

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• add wanted_ids option

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  7258473

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• New class ReadFilter

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  dda42de

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• new method _cdhit_clstr_to_reads

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  ce876cc

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• add run method

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  9780a06

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• Add mah to external progs

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  c93b988

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• New mash wrapper class

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  4d0a56a

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• Fix class name

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  14fd132

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• Return number of reads and total length

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  c0ef9a0

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• return total read and bases counts

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  2d79846

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• Work out closest ref after assembly using mash

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  966dbfd

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• exclude when zero matches

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  f6c8d2e

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• Use mash to get best ref seq

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  9d9964d

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• Use mash to get best ref after assembling

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  faf24f2

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• Always use bowtie2 very-sensitive-local

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  d4ab93e

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• Remove old commented out code

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  3d98fe1

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• open log file earlier. Write references fasta file

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  4ee4b72

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• Use spades --careful by default

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  1b6e879

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• Add mash

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  a94ac4e

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