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Hi all,
Looking for a little bit of advice for performing De novo assemblies on Newbler.
I have sequenced the same genome twice; once with Illumina and once with 454 (both paired end). I have performed a de novo assembly on the 454 data in newbler with relative ease but this yielded poor depth/coverage. I intend to introduce my raw illumina data to this (on newbler) to have a greater chance of reducing my contigs.
I have converted my sol.fastq files to .fasta and ran these alongside the 454 .sff files on newbler. Obviously, .fasta no longer contains the quality data resulting in all reads being assembled with none being excluded. Is there a way for me to use newbler with .fastq files or, alternatively, perform "trimming" of my files to remove failed reads prior to uploading and assembly?
I appreciate any feedback, i'm very new to this.
Lewis
Looking for a little bit of advice for performing De novo assemblies on Newbler.
I have sequenced the same genome twice; once with Illumina and once with 454 (both paired end). I have performed a de novo assembly on the 454 data in newbler with relative ease but this yielded poor depth/coverage. I intend to introduce my raw illumina data to this (on newbler) to have a greater chance of reducing my contigs.
I have converted my sol.fastq files to .fasta and ran these alongside the 454 .sff files on newbler. Obviously, .fasta no longer contains the quality data resulting in all reads being assembled with none being excluded. Is there a way for me to use newbler with .fastq files or, alternatively, perform "trimming" of my files to remove failed reads prior to uploading and assembly?
I appreciate any feedback, i'm very new to this.
Lewis
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