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GitHub / sudarshangc / viral-ngs
Viral genomics analysis pipelines
JSON API: https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sudarshangc%2Fviral-ngs
Fork of broadinstitute/viral-ngs
Stars: 0
Forks: 0
Open Issues: 0
License: other
Language:
Repo Size: 60.1 MB
Dependencies:
80
Created: over 4 years ago
Updated: 10 months ago
Last pushed: over 4 years ago
Last synced: 10 months ago
Files
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Readme
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Dependencies
Dockerfile
docker
- quay.io/broadinstitute/viral-baseimage 0.1.15 build
- attrs =19.1.0 test
- coverage =4.5.2 test
- coveralls =1.3.0 test
- flake8 >=3.2.1 test
- lxml =4.3.3 test
- mock =2.0.0 test
- pycodestyle =2.2.0 test
- pytest =4.2.0 test
- pytest-cov ==2.6.1 test
- pytest-mock =1.10.0 test
- pytest-xdist =1.26.1 test
- six =1.10.0 test
- PyYAML =5.1
- arrow =0.12.1
- bbmap =38.56
- bedtools =2.28.0
- biopython =1.72
- blast =2.7.1
- bmtagger =3.101
- bwa =0.7.17
- cd-hit =4.6.8
- cd-hit-auxtools =4.6.8
- diamond =0.9.10
- fastqc =0.11.7
- future ==0.16.0
- gap2seq =3.1.1a2
- gatk =3.8
- kaiju =1.6.3_yesimon
- kmc =3.1.1rc1
- krakenuniq =0.5.7_yesimon
- krona =2.7.1
- last =876
- lbzip2 =2.5
- lz4-c =1.9.1
- mafft =7.402
- matplotlib =2.2.4
- mummer4 =4.0.0beta2
- muscle =3.8.1551
- mvicuna =1.0
- novoalign =3.07.00
- parallel =20160622
- picard-slim =2.21.1
- pigz =2.4
- prinseq =0.20.4
- pybedtools =0.7.10
- pysam =0.15.0
- r-base =3.5.1
- samtools =1.9
- snpeff =4.3.1t
- spades =3.12.0
- tbl2asn =25.6
- trimmomatic =0.38
- trinity =date.2011_11_26
- unzip =6.0
- vphaser2 =2.0
- PyYAML =5.1
- biopython =1.72
- fastqc =0.11.7
- future ==0.16.0
- lbzip2 =2.5
- lz4-c =1.9.1
- matplotlib =2.2.4
- picard-slim =2.21.1
- pigz =2.4
- pybedtools =0.7.10
- pysam =0.15.0
- samtools =1.9
- unzip =6.0
- PyYAML ==5.1
- Sphinx ==1.4.4
- matplotlib ==2.2.4
- mock >=2.0.0
- sphinx-argparse ==0.1.15
- sphinx_rtd_theme ==0.1.9
requirements-py3.txt
pypi
- boto3 *
- filechunkio >=1.8
- google-cloud-storage *
- pysftp >=0.2.8
- snakemake ==5.6.0