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a set of tools for viral amplicon schemes

License: MIT License

CMake 6.67% C++ 91.84% Python 1.49%

artic amplicon-sequencing viral-genomics nanopore

artic-tools's Introduction

ARTIC tools

a set of tools for working with the ARTIC pipeline

Overview

This collection of tools is being worked on and more utility is due to be added. For now, we have:

download primer schemes and reference sequences
primer scheme validation
alignment softmasking
vcf filtering

Read the docs for more info and checkout the ARTIC pipeline.

Install

conda

conda install -c bioconda artic-tools

source

You need CMake, Boost, HTSlib and a C++17 compiler. To download and install artic-tools run:

git clone --recursive https://github.com/will-rowe/artic-tools.git
mkdir artic-tools/build
cd artic-tools/build
cmake ..
make -j4
make test
../bin/artic-tools -h

artic-tools's People

Contributors

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jts biowilko

artic-tools's Issues

deduplicate variants called in multiple primer pools

Thinking about this in response to: artic-network/fieldbioinformatics#53

At the moment, artic-tools check_vcf will find variants in overlap regions and check for multiple copies. If only one copy is found it is marked as potential contamination and then dropped. If multiple copies are found, it is marked as a pass and all copies are kept.

It would be good to have an option added so that where multiple copies are found, they are collapsed and reported as a single var.

command artic-tools get_scheme don't work

Hi developer,

I am try to use artic-tools for doing some task. When I use the command:

artic-tools get_scheme nCoV-2019 --schemeVersion 3

or --schemeVersion 2 or --schemeVersion 3, only downloaded the files .primer.bed and .reference.fasta. The files .insert.bed and .tsv is not downloaded.

Thanks,

--strict fails

--strict fails for every sample in a recent run, looks like a bug with the contig missing from the vcf header which is causing vcf_parse to fail.

Content of vcfreport.txt:

[16:35:15] [artic-tools::check_vcf] starting VCF checker
[16:35:15] [artic-tools::check_vcf] reading scheme
[16:35:15] [artic-tools::check_vcf] collecting scheme stats
[16:35:15] [artic-tools::check_vcf]   primer scheme file:   ./primer-schemes/scov2/V3/scov2.scheme.bed
[16:35:15] [artic-tools::check_vcf]   reference sequence:   MN908947.3
[16:35:15] [artic-tools::check_vcf]   number of pools:    2
[16:35:15] [artic-tools::check_vcf]   number of primers:   218 (includes 22 alts)
[16:35:15] [artic-tools::check_vcf]   minimum primer size:  22
[16:35:15] [artic-tools::check_vcf]   maximum primer size:  57
[16:35:15] [artic-tools::check_vcf]   number of amplicons:  98
[16:35:15] [artic-tools::check_vcf]   mean amplicon size:   343
[16:35:15] [artic-tools::check_vcf]   maximum amplicon size: 375
[16:35:15] [artic-tools::check_vcf]   scheme ref. span:    30-29866
[16:35:15] [artic-tools::check_vcf]   scheme overlaps:    12.850247%
[16:35:15] [artic-tools::check_vcf] checking VCF file
[16:35:15] [artic-tools::check_vcf]   filtering variants: true
[16:35:15] [artic-tools::check_vcf]   output file: SAMP_ID.merged.filtered.vcf
[16:35:15] [artic-tools::check_vcf]   discard primer site vars: true
[16:35:15] [artic-tools::check_vcf]   discard overlap fail vars: true
[W::vcf_parse] Contig 'MN908947.3' is not defined in the header. (Quick workaround: index the file with tabix.)
error--> refusing to process VCF records

Specifically the command failing on standard error is reported by artic minion as:

Command failed:artic-tools check_vcf --dropPrimerVars --dropOverlapFails --vcfOut SAMP_ID.merged.filtered.vcf SAMP_ID.merged.vcf ./primer-schemes/scov2/V3/scov2.scheme.bed 2> SAMP_ID.vcfreport.txt

Conda release for 0.3.1

Hello,

Our lab wants to switch to 0.3.1 to avoid the segfault issue with 0.3.0 that was patched, but it looks like it's not available in conda yet.

Thanks,
Jake

`make install` installs everything but the binary

I just built artic-tools on our cluster and was surprised to see a make install present, but it only installs various libs and includes, not the binary.

I built artic-tools from git tag 0.3.1 like this:

$ cmake .. -DHTS_LIB=/global/apps/htslib/1.15.1/lib/libhts.so -DHTS_INCLUDE_DIR=/global/apps/htslib/1.15.1/include/ -DCMAKE_INSTALL_PREFIX=/global/apps/artic-tools/0.3.1
$ make -j4
$ make test
$ make install

The README.md actually implies that we only need to copy the binary so maybe this install target could be removed? Leaving this issue here for future travelers who don't use conda. Thank you!

Compilation error

During a recent migration on Bioconda I ran into the following compilation error on OSX using clang:

2022-10-01T20:52:03.9518190Z 20:52:03 BIOCONDA INFO (ERR) /Users/runner/miniconda/conda-bld/artic-tools_1664657237571/work/extlibs/googletest/googlemock/include/gmock/gmock-actions.h:455:3: error: definition of implicit copy constructor for 'PolymorphicAction<testing::internal::ReturnVoidAction>' is deprecated because it has a user-declared copy assignment operator [-Werror,-Wdeprecated-copy]
2022-10-01T20:52:03.9572120Z 20:52:03 BIOCONDA INFO (ERR)   GTEST_DISALLOW_ASSIGN_(PolymorphicAction);
2022-10-01T20:52:03.9626720Z 20:52:03 BIOCONDA INFO (ERR)   ^
2022-10-01T20:52:03.9707650Z 20:52:03 BIOCONDA INFO (ERR) /Users/runner/miniconda/conda-bld/artic-tools_1664657237571/work/extlibs/googletest/googletest/include/gtest/internal/gtest-port.h:682:8: note: expanded from macro 'GTEST_DISALLOW_ASSIGN_'
2022-10-01T20:52:03.9748850Z 20:52:03 BIOCONDA INFO (ERR)   void operator=(type const &) = delete
2022-10-01T20:52:03.9802820Z 20:52:03 BIOCONDA INFO (ERR)        ^
2022-10-01T20:52:03.9849190Z 20:52:03 BIOCONDA INFO (ERR) /Users/runner/miniconda/conda-bld/artic-tools_1664657237571/work/extlibs/googletest/googlemock/include/gmock/gmock-actions.h:1016:10: note: in implicit copy constructor for 'testing::PolymorphicAction<testing::internal::ReturnVoidAction>' first required here
2022-10-01T20:52:03.9924530Z 20:52:03 BIOCONDA INFO (ERR)   return MakePolymorphicAction(internal::ReturnVoidAction());
2022-10-01T20:52:04.0025640Z 20:52:03 BIOCONDA INFO (ERR)          ^

Any ideas how to resolve this?