.gitignore
.readthedocs.yaml
INSTALL.rst
LICENSE
MANIFEST.in
NEWS.rst
README.rst
bitbucket-pipelines.yml
pyproject.toml
requirements.txt
setup.py
bin/AlignSets.py
bin/AssemblePairs.py
bin/BuildConsensus.py
bin/ClusterSets.py
bin/CollapseSeq.py
bin/ConvertHeaders.py
bin/EstimateError.py
bin/FilterSeq.py
bin/MaskPrimers.py
bin/PairSeq.py
bin/ParseHeaders.py
bin/ParseLog.py
bin/SplitSeq.py
bin/UnifyHeaders.py
docs/Makefile
docs/api.rst
docs/conf.py
docs/doc_requires.txt
docs/index.rst
docs/info.rst
docs/install.rst
docs/news.rst
docs/overview.rst
docs/usage.rst
docs/_static/immcantation.ico
docs/_static/immcantation.png
docs/_static/overrides.css
docs/_static/presto.png
docs/examples/annotations.rst
docs/examples/assembly.rst
docs/examples/filter.rst
docs/examples/import.rst
docs/examples/primers.rst
docs/examples/umi.rst
docs/modules/Annotation.rst
docs/modules/Applications.rst
docs/modules/Commandline.rst
docs/modules/IO.rst
docs/modules/Multiprocessing.rst
docs/modules/Sequence.rst
docs/tools/AlignSets.rst
docs/tools/AssemblePairs.rst
docs/tools/BuildConsensus.rst
docs/tools/ClusterSets.rst
docs/tools/CollapseSeq.rst
docs/tools/ConvertHeaders.rst
docs/tools/EstimateError.rst
docs/tools/FilterSeq.rst
docs/tools/MaskPrimers.rst
docs/tools/PairSeq.rst
docs/tools/ParseHeaders.rst
docs/tools/ParseLog.rst
docs/tools/SplitSeq.rst
docs/tools/UnifyHeaders.rst
docs/tools/tool_summary.tsv
docs/workflows/Greiff2014_Workflow.rst
docs/workflows/Jiang2013_Workflow.rst
docs/workflows/Stern2014_Workflow.rst
docs/workflows/VanderHeiden2017_Workflow.rst
docs/workflows/data/IGHC.fasta
docs/workflows/figures/Greiff2014_Flowchart.svg
docs/workflows/figures/Greiff2014_ReadConfiguration.svg
docs/workflows/figures/Jiang2013_Flowchart.svg
docs/workflows/figures/Jiang2013_ReadConfiguration.svg
docs/workflows/figures/Primer_Alignment.svg
docs/workflows/figures/Stern2014_Flowchart.svg
docs/workflows/figures/Stern2014_ReadConfiguration.svg
docs/workflows/figures/VanderHeiden2017_Flowchart.svg
docs/workflows/figures/VanderHeiden2017_ReadConfiguration.svg
docs/workflows/scripts/Greiff2014_Commands.sh
docs/workflows/scripts/Jiang2013_Commands.sh
docs/workflows/scripts/Stern2014_Commands.sh
docs/workflows/scripts/VanderHeiden2017_Commands.sh
docs/workflows/tables/454_Jiang2013_Performance.tsv
docs/workflows/tables/MiSeq_Stern2014_Performance.tsv
examples/Greiff2014/ExamplePipeline_Greiff2014.sh
examples/Greiff2014/Greiff2014_CPrimers.fasta
examples/Greiff2014/Greiff2014_Flowchart.vsdx
examples/Greiff2014/Greiff2014_ReadConfiguration.vsdx
examples/Greiff2014/Greiff2014_VPrimers.fasta
examples/Greiff2014/README.rst
examples/Jiang2013/ExamplePipeline_Jiang2013.ps1
examples/Jiang2013/ExamplePipeline_Jiang2013.sh
examples/Jiang2013/Jiang2013_Flowchart.vsdx
examples/Jiang2013/Jiang2013_ReadConfiguration.vsdx
examples/Jiang2013/README.rst
examples/Jiang2013/SRR765688_MIDs.fasta
examples/Jiang2013/SRX190717_CPrimers.fasta
examples/Jiang2013/SRX190717_VPrimers.fasta
examples/Stern2014/ExamplePipeline_Stern2014.sh
examples/Stern2014/README.rst
examples/Stern2014/Stern2014_CPrimers.fasta
examples/Stern2014/Stern2014_Flowchart.vsdx
examples/Stern2014/Stern2014_ReadConfiguration.vsdx
examples/Stern2014/Stern2014_VPrimers.fasta
examples/VanderHeiden2017/AbSeq_Human_IG_InternalCRegion.fasta
examples/VanderHeiden2017/AbSeq_R1_Human_IG_Primers.fasta
examples/VanderHeiden2017/AbSeq_R2_TS.fasta
examples/VanderHeiden2017/ExamplePipeline_VanderHeiden2017.sh
examples/VanderHeiden2017/IMGT_Human_IG_V.fasta
examples/VanderHeiden2017/README.rst
examples/VanderHeiden2017/VanderHeiden2017_Flowchart.vsdx
examples/VanderHeiden2017/VanderHeiden2017_ReadConfiguration.vsdx
presto/Annotation.py
presto/Applications.py
presto/Commandline.py
presto/Defaults.py
presto/IO.py
presto/Multiprocessing.py
presto/Sequence.py
presto/Version.py
presto/__init__.py
presto.egg-info/PKG-INFO
presto.egg-info/SOURCES.txt
presto.egg-info/dependency_links.txt
presto.egg-info/not-zip-safe
presto.egg-info/requires.txt
presto.egg-info/top_level.txt
tests/__init__.py
tests/test_Annotation.py
tests/test_AssemblePairs.py
tests/test_BuildConsensus.py
tests/test_ClusterSets.py
tests/test_CollapseSeq.py
tests/test_ConvertHeaders.py
tests/test_EstimateError.py
tests/test_IO.py
tests/test_MaskPrimers.py
tests/test_Sequence.py
tests/test_UnifyHeaders.py
tests/data/clusters.fasta
tests/data/head.fasta
tests/data/select.txt
tests/data/tail.fasta