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TraCeR
A computational method to reconstruct full-length, paired T cell receptor (TCR) sequences from T lymphocyte single-cell RNA sequence data. TraCeR links T cell specificity with functional response by revealing clonal relationships between cells alongside their transcriptional profiles. TraCeR extracts TCR-derived sequencing reads for each cell by alignment against ‘combinatorial recombinomes’ comprising all possible combinations of V and J segments. Reads are then assembled into contiguous sequences that are analyzed to find full-length, recombined TCR sequences. Importantly, the reconstructed recombinant sequences typically contain nearly the complete length of the TCR V(D)J region and so allow high-confidence discrimination between closely related gene segments. Our method is sensitive, accurate and easy to adapt to any species for which annotated TCR gene sequences are available.
CEL-Seq
CEL-Seq provides its first single-cell, on-chip barcoding method, and we detected gene expression changes accompanying the progression through the cell cycle in mouse fibroblast cells. The pipeline consists of the following steps: (1) demultiplexing: using the barcode from R1 we split R2 reads into their original samples creating a separate file for each sample. Since the unique molecular identifier (UMI) is also read in R1 we extract it and attach it to the R2 read metadata for downstream analysis; (2) mapping: using Bowtie2, we map the reads of the different samples in parallel, cutting the analysis time by roughly the number of available cores; (3) read counting: A modified version of the htseq-count script that supports the identification and elimination of reads sharing the same UMI to generate an accurate molecule count for each feature. We use binomial statistics to convert the number of UMIs into transcript counts. The different steps in the pipeline are wrapped together in a single program with a simple configuration file allowing to control for different run modes.
Dr.seq
Allows quality control (QC) and analysis components of parallel single cell transcriptome and epigenome data. Dr.seq is a quality control (QC) and analysis pipeline that provides both multifaceted QC reports and cell clustering results. Parallel single cell transcriptome data generated by different technologies can be transformed to the standard input with contained functions. Using relevant commands, the software can also be used to report quality measurements based on four aspects and can generate detailed analysis results for scATAC-seq and Drop-ChIP datasets.
Falco
A cloud-based framework designed for multi-sample analysis of transcriptomic data in an efficient and scalable manner. Falco utilises state-of-the-art big data technology of Apache Hadoop and Apache Spark to perform massively parallel alignment, quality control, and feature quantification of single-cell transcriptomic data in Amazon Web Service (AWS) cloud-computing environment. We have evaluated the performance of Falco using two public scRNA-seq datasets and demonstrated Falco's scalability. The result shows Falco performs at least 2.6x faster against a highly optimized single node analysis and a reduction in runtime with increasing number of computing nodes. Falco also allows user to the utilise low-cost spot instances of AWS, providing a 65% reduction in cost of analysis.
zUMIs
Processes raw reads to count tables for RNA-seq data using Unique Molecular Identifiers (UMIs). zUMIs is a pipeline applicable for most experimental designs of RNA-seq data, such as single-nuclei sequencing techniques. This method allows for down sampling of reads before summarizing UMIs per feature, which is recommended for cases of highly different read numbers per sample. zUMIs is flexible with respect to the length and sequences of the barcodes (BCs) and UMIs, making it compatible with a large number of protocols.
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