RNA-Seq Assembly

Bridger is an efficient de novo transcriptome assembler for RNA-Seq data. It expects as input RNA-Seq reads (single or paired) in fasta or fastq format, outputs all transcripts in fasta format, without using a reference genome. Briefly, it works in two steps: First, Bridger partitions the sequence data into many individual splicing graphs, each capturing the full transcriptional complexity at a given gene or no more than a few genes. Then, for each splicing graph, Bridger uses a rigorous mathematical model called minimum path cover to search an optimal set of paths (transcripts) that can be supported by sequence data and could explain all observed splicing events of each locus.