These are not online, but can be helpful.
1) check this biostar How To Remove The Same Sequences In The Fasta Files? to remove exact duplicate sequences.
2) If you want to remove sequences based on similarity cutoff, you can try cd-hit-est, uclust etc.
Poor quality sequences
1) If you have reads, then you can map those reads using some mapping tools such as bowtie, BWA and check if the sequence has sufficient coverage or not. Those with insufficient must be of poor quality.