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Getting Started

  • Overview
  • Download
  • Installation
  • Release Notes

Usage Documentation

  • Commandline Usage
    • AlignSets.py
    • AssemblePairs.py
    • BuildConsensus.py
    • ClusterSets.py
    • CollapseSeq.py
    • ConvertHeaders.py
    • EstimateError.py
    • FilterSeq.py
    • MaskPrimers.py
    • PairSeq.py
    • ParseHeaders.py
    • ParseLog.py
    • SplitSeq.py
    • UnifyHeaders
  • API

Example Workflows

  • Roche 454 BCR mRNA with Multiplexed Samples
  • Illumina MiSeq 2x250 BCR mRNA
  • UMI Barcoded Illumina MiSeq 2x250 BCR mRNA
  • UMI Barcoded Illumina MiSeq 325+275 paired-end 5’RACE BCR mRNA

Example Tasks

  • Importing Data
  • Manipulating Annotations
  • Filtering and Subsetting
  • Isotype and Primer Annotations
  • Fixing Assembly Problems
  • Fixing UMI Problems

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Commandline Usage¶

  • AlignSets.py
    • AlignSets.py muscle
    • AlignSets.py offset
    • AlignSets.py table
  • AssemblePairs.py
    • AssemblePairs.py align
    • AssemblePairs.py join
    • AssemblePairs.py reference
    • AssemblePairs.py sequential
  • BuildConsensus.py
  • ClusterSets.py
    • ClusterSets.py all
    • ClusterSets.py barcode
    • ClusterSets.py set
  • CollapseSeq.py
  • ConvertHeaders.py
    • ConvertHeaders.py 454
    • ConvertHeaders.py genbank
    • ConvertHeaders.py generic
    • ConvertHeaders.py illumina
    • ConvertHeaders.py imgt
    • ConvertHeaders.py migec
    • ConvertHeaders.py sra
  • EstimateError.py
    • EstimateError.py barcode
    • EstimateError.py set
  • FilterSeq.py
    • FilterSeq.py length
    • FilterSeq.py maskqual
    • FilterSeq.py missing
    • FilterSeq.py quality
    • FilterSeq.py repeats
    • FilterSeq.py trimqual
  • MaskPrimers.py
    • MaskPrimers.py align
    • MaskPrimers.py extract
    • MaskPrimers.py score
  • PairSeq.py
  • ParseHeaders.py
    • ParseHeaders.py add
    • ParseHeaders.py collapse
    • ParseHeaders.py copy
    • ParseHeaders.py delete
    • ParseHeaders.py expand
    • ParseHeaders.py merge
    • ParseHeaders.py rename
    • ParseHeaders.py table
  • ParseLog.py
  • SplitSeq.py
    • SplitSeq.py count
    • SplitSeq.py group
    • SplitSeq.py sample
    • SplitSeq.py samplepair
    • SplitSeq.py select
    • SplitSeq.py sort
  • UnifyHeaders
    • UnifyHeaders consensus
    • UnifyHeaders delete
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© Copyright Kleinstein Lab, Yale University, 2021. Revision b503b521.

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