Project one: Genome assembly using two-generation data (local assembly and global Assembly)

Project data:

• Kongyu_131_pcrfree_. CCAAT_L006_R1_001.fastq.gz (100X) (19G)
  Kongyu_131_pcrfree_. CCAAT_L006_R2_001.fastq.gz (100X) (20G)
  
• Y255_pcrfree_. TCCGC_L005_R1_001.fastq.gz (30X) (5.4G)
  Y255_pcrfree_. TCCGC_L005_R2_001.fastq.gz (30X) (6.0G)
• All.chrs.con.fasta (364M)

Tools:

• BWA
• IGV
• Soapdenovo

Strategy:

• The sequenced second-generation reads used BWA to the reference genome, divided into different windows, partially assembled by the window, and then merged.

Pre-Knowledge:

• Ability to write scripts using Perl and Shell skillfully
• will be proficient in using PBS to submit tasks
• Bwa How to use
• IGV How to use
• Soapdenovo How to use

Problems with local assembly:

There are already two groups of people did not come out, the local assembly is mostly impossible to assemble a complete 100K window, because the second generation sequence reads too short, repeat the sequence too much, repeat the sequence will cause the connection is interrupted, a window will appear a lot of fragments, and there is no way to continue to connect them, so they are halfway.

In the following situations, it is necessary to connect many fragments into a complete sequence by means of later analysis.

To Fat's article, completely in the absence of a reference genome, Denovo assembled, using a variety of means, to assemble fragmented sequences into complete genomes.

The boss does not know much, the biggest contribution is to urge.

Project one: Genome assembly using two-generation data (local assembly and global Assembly)