Quast Ouput

Question

[kishorssf91]

Hi, I have done a assembly statistics of a transcriptome assembly. I have found 102072 headers (">") and for that simply i thought that my assmbly has 102072 transcripts and i also considered one transcript as one contig. But when i run the quast i found in somewhere another number for contigs (47484). Hence i am confused how many contigs i have actually. Here, i am adding a picture for that for easy going.May be its a very basic question to most of the people but very important for my understanding. I hope i will receive help from you. Thanks.

Answer 1

[Ying]

The "# contigs 47484" is based on contig of size >= 500 bp (see the first line of your screenshot). The "# contigs (>= 0 bp)" is the raw number of contigs (i.e. 102072 as you counted the headers).