I have 3 Illumina paired-end sequencing data of humans. I want to assemble these 3 genomes. My final goal is to retrieve some gene sequences from these 3 genomes.
So,
1) Please suggest to me any pipelines or papers that can help to assemble these genomes.
2) Can I retrieve some specific gene sequence from these assembled genomes? If yes, please suggest me a way to do it.
3) If no, Is there any other alternative??
A big thank you in advance...
Sir, @Pratanu kayet actually I'm just trying to find this as a student , I don't have much information about this, so sorry...
1. There are many pipelines available to assemble Illumina paired-end sequencing data into a genome assembly, including SPAdes, ABySS, SOAPdenovo, and Canu. The choice of pipeline depends on factors such as the size and complexity of the genome, the quality and length of the reads, and the computational resources available. A good starting point would be to use a well-established pipeline such as SPAdes, which has been widely used for genome assembly.
2. Yes, you can retrieve specific gene sequences from the assembled genomes. One common approach is to use a gene prediction tool such as GeneMark, AUGUSTUS, or SNAP to identify the gene locations within the assembly. Then you can extract the corresponding sequences using a tool such as BedTools or Samtools.
3. If you cannot retrieve the desired gene sequences from the assembled genome, another alternative would be to re-sequence the target genes using a targeted sequencing approach such as PCR-based amplicon sequencing or hybridization-based capture sequencing. These approaches allow you to selectively amplify and sequence the genes of interest, rather than the entire genome.
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