Maps short reads to a reference sequence. Phasemhc combines de novo assemblies with transmission information and read backed phasing. It was tested by simulating reads in an artificial trio with known Major Histocompatibility Complex (MHC) haplotypes, reconstructing the haplotypes and comparing these to the original haplotypes. This tool permits to study novel sequences using mapping-based approaches and will enable to place them more accurately in the reference genome.
Identifies novel sequences in a de novo human genome assembly. NSIT offers a graphical viewer to assist in studying the overlap of novel sequences with other set of selected sequences. It permits quick visual inspection of sequence contamination. This tool follows three steps: (1) k-mer hash table construction, (2) chromosome assignment, and (3) query alignment. It is capable of aligning de novo sequences to the reference genome.
Enables to map reads on branching paths of the de Bruijn graph (DBG). BGREAT is designed for mapping reads on branching paths of a compacted (DBG), using reasonable resources both in terms of time and memory. Our approach follows the usual “seed and extend” paradigm. More generally, the proposed implementation applies heuristic schemes, both regarding the indexing and the alignment phases. The availability of BGREAT opens the door to its application to fundamental tasks such as read error correction, read compression, variant quantification, or haplotype reconstruction.
RAUR is to re-align the reads that can not be mapped by alignment tools. It takes advantages of the base quality scores (reported by the sequencer) to figure out the longest segment of a read with at most K low quality bases. Combined with an alignment tool (like bwa or bowtie2), RAUR re-align the trimmed reads.
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