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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.