Transcriptome Assembly

1. BinPacker is an efficient de novo trascriptome assembler for RNA-Seq data. It can assemble all transcripts from short reads (single or paired) without using a reference. The software expects as input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Briefly, it works in two step: first, BinPacker 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 BinPacker uses variants of the traditional bins packing model to search for minimum edge-path-cover over the splicng graph that can be supported by our data and could explain all observed splicing events of each locus. This software is free to use, modify, redistribute without any restrictions, except including the license provided with the distribution. ............................................................................................. 2. TransComb is an efficient ab initio trascriptome assembler for RNA-Seq data. It can assemble all transcripts from short paired-end reads using a reference and analyze their abundances. The software expects as input alignment file by Tophat2 BAM format, and ouput all assembled candidate transcripts in gtf format. This software is free to use, modify, redistribute without any restrictions, except including the license provided with the distribution.