Mercurial > repos > galaxy-australia > hifiadapterfilt

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"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit db087ed782a52833a02df3bfef0793b4dd909081"
author galaxy-australia
date Wed, 16 Nov 2022 06:19:15 +0000
parents bbc2060caa0e
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bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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1 # HiFiAdapterFilt
bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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2 Remove CCS reads with remnant PacBio adapter sequences and convert outputs to a compressed .fastq (.fastq.gz).
bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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4 # Dependencies
bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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5 - BamTools
bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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6 - BLAST+
bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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8 # Installation
bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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9 Currently only tested on Ubuntu
bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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11 # Docker
bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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12 - HiFiAdapterFilt Docker is available on https://hub.docker.com/r/dmolik/pbadapterfilt
bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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14 ```
bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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15 docker pull dmolik/pbadapterfilt
bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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16 docker run -t -d -v /hifireads_data_directory_on_host_machine/:/home/genomics/HiFiAdapterFilt-master/ubuntu --name hifiadapterfilt dmolik/pbadapterfilt
bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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17 docker exec -it <container_id> /bin/bash
bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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19 ```
bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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bbc2060caa0e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
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21 See [official documentation](https://github.com/sheinasim/HiFiAdapterFilt) for more details.