Singularity sif container containing Nanopore Medaka software for Medaka docker downloaded 2023-06-17 from git clone https://github.com/nanoporetech/medaka.git
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| Format: | Recurso digital |
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2025
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| _version_ | 1866902089173565440 |
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| author | Rath, Emma M. |
| author_facet | Rath, Emma M. |
| contents | <p>Singularity sif container containing Nanopore Medaka software for Medaka docker downloaded 2023-06-17 from git clone https://github.com/nanoporetech/medaka.git</p> <p>This Singularity sif container containing Nanopore Medaka software was created from Medaka docker downloaded 2023-06-17 from git clone https://github.com/nanoporetech/medaka.git</p> <p>Please read https://github.com/nanoporetech/medaka.git and ensure that you are permitted to use the Medaka docker container before using this Singularity container created from the docker container.</p> <p>If you use this Medaka singularity container, please attribute it as you would for use of the Medaka docker container.</p> <p>The purpose of this Medaka container is to allow quick installation onto a local laboratory computer of the pipeline for analysing Nanopore sequencing data of bacterial infection DNA at https://github.com/emmamrath/pipeline_for_analysing_Nanopore_sequencing_of_infection_DNA</p> <p>Installation of software onto a local laboratory computer is necessary when sequenced DNA samples from human patients could contain human DNA and thus the laboratory does not have ethics approval to upload these samples to cloud services for analysis.</p> <p>Here is an example of how to use this container on a linux platform:</p> <p># Run Medaka to polish Nanopore DNA sequencing data contained in a FASTQ file that has already had consensus sequence(s) built for it in a FASTA file by Metaflye<br>indir_fastq=/my/input/directory/containing/sample/fastq/file<br>indir_draft_assembly=/my/input/directory/containing/metaflye/output/for/this/sample/"${sample}"<br>outdir=/my/medaka/output/directory/output/for/this/sample/"\${sample}"<br>NPROC=1<br>BASECALLS=/mnt1/"\${sample}".fastq.gz<br>DRAFT=/mnt2/assembly.fasta<br>OUTDIR=/mnt_out/medaka_consensus<br>singularity exec --bind "\${indir_fastq}":/mnt1,"\${indir_draft_assembly}":/mnt2,"\${outdir}":/mnt_out \<br> medaka_singularity.sif \<br> env PATH=/medaka/venv/bin:\$PATH /medaka/venv/bin/medaka_consensus -i \${BASECALLS} -d \${DRAFT} -o \${OUTDIR} -t \${NPROC} -m r941_min_high_g303</p> <p> </p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_15250562 |
| institution | Zenodo |
| language | |
| publishDate | 2025 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | Singularity sif container containing Nanopore Medaka software for Medaka docker downloaded 2023-06-17 from git clone https://github.com/nanoporetech/medaka.git Rath, Emma M. <p>Singularity sif container containing Nanopore Medaka software for Medaka docker downloaded 2023-06-17 from git clone https://github.com/nanoporetech/medaka.git</p> <p>This Singularity sif container containing Nanopore Medaka software was created from Medaka docker downloaded 2023-06-17 from git clone https://github.com/nanoporetech/medaka.git</p> <p>Please read https://github.com/nanoporetech/medaka.git and ensure that you are permitted to use the Medaka docker container before using this Singularity container created from the docker container.</p> <p>If you use this Medaka singularity container, please attribute it as you would for use of the Medaka docker container.</p> <p>The purpose of this Medaka container is to allow quick installation onto a local laboratory computer of the pipeline for analysing Nanopore sequencing data of bacterial infection DNA at https://github.com/emmamrath/pipeline_for_analysing_Nanopore_sequencing_of_infection_DNA</p> <p>Installation of software onto a local laboratory computer is necessary when sequenced DNA samples from human patients could contain human DNA and thus the laboratory does not have ethics approval to upload these samples to cloud services for analysis.</p> <p>Here is an example of how to use this container on a linux platform:</p> <p># Run Medaka to polish Nanopore DNA sequencing data contained in a FASTQ file that has already had consensus sequence(s) built for it in a FASTA file by Metaflye<br>indir_fastq=/my/input/directory/containing/sample/fastq/file<br>indir_draft_assembly=/my/input/directory/containing/metaflye/output/for/this/sample/"${sample}"<br>outdir=/my/medaka/output/directory/output/for/this/sample/"\${sample}"<br>NPROC=1<br>BASECALLS=/mnt1/"\${sample}".fastq.gz<br>DRAFT=/mnt2/assembly.fasta<br>OUTDIR=/mnt_out/medaka_consensus<br>singularity exec --bind "\${indir_fastq}":/mnt1,"\${indir_draft_assembly}":/mnt2,"\${outdir}":/mnt_out \<br> medaka_singularity.sif \<br> env PATH=/medaka/venv/bin:\$PATH /medaka/venv/bin/medaka_consensus -i \${BASECALLS} -d \${DRAFT} -o \${OUTDIR} -t \${NPROC} -m r941_min_high_g303</p> <p> </p> |
| title | Singularity sif container containing Nanopore Medaka software for Medaka docker downloaded 2023-06-17 from git clone https://github.com/nanoporetech/medaka.git |
| url | https://doi.org/10.5281/zenodo.15250562 |