Pinned Repositories
ARTIC_SARS-CoV-2
Supplementary information for the Lexogen SARS-CoV2 ARTIC primer panel
bamread
Bam to Pandas DataFrame, quickly
corall_analysis
Standard analysis routine for samples generated with Corall and Corall v2 library preparation kit.
Fastq-Read-ID-Converter
idemux
Idemux is a command line tool designed to demultiplex paired-end fastq files from QuantSeq-Pool.
idemuxcpp
iDemux is an all-in-one command line tool that can be used for both demultiplexing and error correction of FASTQ files. It enables demultiplexing of i1 inline barcodes of Lexogen’s QuantSeq-Pool as well as demultiplexing of i7 and/or i5 indices of any other RNA-Seq library prep. iDemux can also be used for superior error correction of RNA-Seq libraries generated with Lexogen’s UDI 12 nt Unique Dual Indices. This C++ version is faster than the Python version but requires a certain proficiency in command line tool handling.
pyranges
Performant Pythonic GenomicRanges
quantseqpool_analysis
Standard analysis routine for samples that were generated with Lexogen's QuantSeq pool library preparation kit.
sars-cov-2_analysis
An analysis script routine to assess if samples that were prepared with Lexogen's barcoded targeted QuantSeq Flex library preparation contain copies of the SARS-CoV-2 virus.
SIRVsuite
SIRVsuite is a command line tool to QC an RNA-Seq workflow using Lexogen's SIRV spike-in controls.
Lexogen's Repositories
Lexogen-Tools/idemux
Idemux is a command line tool designed to demultiplex paired-end fastq files from QuantSeq-Pool.
Lexogen-Tools/SIRVsuite
SIRVsuite is a command line tool to QC an RNA-Seq workflow using Lexogen's SIRV spike-in controls.
Lexogen-Tools/idemuxcpp
iDemux is an all-in-one command line tool that can be used for both demultiplexing and error correction of FASTQ files. It enables demultiplexing of i1 inline barcodes of Lexogen’s QuantSeq-Pool as well as demultiplexing of i7 and/or i5 indices of any other RNA-Seq library prep. iDemux can also be used for superior error correction of RNA-Seq libraries generated with Lexogen’s UDI 12 nt Unique Dual Indices. This C++ version is faster than the Python version but requires a certain proficiency in command line tool handling.
Lexogen-Tools/quantseqpool_analysis
Standard analysis routine for samples that were generated with Lexogen's QuantSeq pool library preparation kit.
Lexogen-Tools/corall_analysis
Standard analysis routine for samples generated with Corall and Corall v2 library preparation kit.
Lexogen-Tools/ARTIC_SARS-CoV-2
Supplementary information for the Lexogen SARS-CoV2 ARTIC primer panel
Lexogen-Tools/bamread
Bam to Pandas DataFrame, quickly
Lexogen-Tools/Fastq-Read-ID-Converter
Lexogen-Tools/pyranges
Performant Pythonic GenomicRanges
Lexogen-Tools/sars-cov-2_analysis
An analysis script routine to assess if samples that were prepared with Lexogen's barcoded targeted QuantSeq Flex library preparation contain copies of the SARS-CoV-2 virus.