Schematic diagram of L_RNA_scaffolder steps. A schematic diagram of L_RNA_scaffolder steps illustrating the selection of ‘guide’ transcripts, ordering the fragments and building paths. i) Transcripts (green) are aligned to genomic fragments (black). The genome incompleteness results in that the transcripts are not fully covered and separated into different fragments. ii) The transcripts not fully covered are selected as ‘guides’. All alignment query regions are ordered based on their start positions in the read and are clustered into different blocks. iii) All query regions are attributed to different blocks. One block is represented by the longest query region in it. iv) All blocks are ordered according to their coordinates in the read. v) The genome fragments corresponding to the blocks are sorted following block order. vi) The DNA sequence between two neighboring blocks is a potential intron (orange). The program filters the fragment connection where the intron is extremely large. vii) One fragment might be as the start and/or end in many connections. Every read (arc) stands for supporting evidence connecting the two fragments. The start fragments are assigned to the connection with the most supporting reads. The same is done for the end fragments. One fragment is attributed to at most two connections. viii) A scaffolding path consists of at least two fragments, one predecessor and one terminator. Some paths have crossover points. Finally, all fragments are attributed into paths.