Hi!
I'm looking for a program that can assemble paired end (100bpx2 HiSeq) reads without making contigs. The reads are from amplicons that vary from 49bp to 154bp; the amplicons are from plants and animals. I've already removed the adapters with Cutadapt. I've tried Pandaseq, but it misses a lot of reads. Coperead expects the reads to be the same length. Trimmomatic wasn't stringent enough for removing adapters, so its out too .
If anyone could suggest a program or even a perl script that will put the read 1 and read 2 together, preferably while using the phred scores and give me a fastq file, that would be lovely.
I'm looking for a program that can assemble paired end (100bpx2 HiSeq) reads without making contigs. The reads are from amplicons that vary from 49bp to 154bp; the amplicons are from plants and animals. I've already removed the adapters with Cutadapt. I've tried Pandaseq, but it misses a lot of reads. Coperead expects the reads to be the same length. Trimmomatic wasn't stringent enough for removing adapters, so its out too .
If anyone could suggest a program or even a perl script that will put the read 1 and read 2 together, preferably while using the phred scores and give me a fastq file, that would be lovely.
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