Why many large genomes were sequenced without assemblies or their assembly levels are just contig, such as sequences in 1000 genomes project

Question

[nonaddldy]

If I want to analyze human Y genome at chromsome level, is it difficult to assemble the publised human y sequences at this level and how should I prepare to assembly them?

[JC]

If you are talking about known mapping reads to genomes like the human genome, the 1000 Genomes Project gives you the detected variants in VCFs, then you can prepare an individual genome patching the reference genome with all the reported variants. There is no need to provide for each individual their genome as Fasta.

If you want to de novo assembly using the raw reads, you will find there is not enough coverage to have a full reconstruction, you will need to sequence deeper or combine technologies (short + long reads) to get better contigs. In the past weeks, there was a report of sequencing chromosome X in one pass.

[nonaddldy]

Thanks for your advice, so I decide to apply the VCF files, and the staff of 1000 genome project e-mailed us that UCSC genome browser can also help us to investigate the sequence.