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who are using Euler SR , can give some suggestions? i assembly 75bp reads with it .
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What questions do you have?Originally posted by xzk421 View Post -
A few recommendations for assembling Illumina reads with euler-sr:
1. Pre-filter for A-saturated reads:
$EUSRC/assembly/$MACHTYPE/filterIllumina reads.fasta reads.fasta.filt
2. Put all reads to assemble into one file. Every fasta title should be unique in this file.
3. If your reads are paired (and they are stored in a file reads.fasta), check the reads.fasta.mates to see if the regular expressions used to match reads worked. If no reads were matched, all entries will be "-1 -1".
4. Assembly quality varies with the following:
1. error rate
2. repeat content of the genome
3. coverage
To check to see if you had low coverage, or a very high error rate that fragmented the genome, run the graph summary program:
$EUSRC/assembly/$MACHTYPE/printGraphSummary matetransformed/reads.fasta -sources
This will print all the lengths of contigs that are fragmented due to low coverage or sequencing errors (probably low coverage). If this high relative to the number of contigs in the assembly, either use a smaller vertex size for assembly, or run more reads.Comment
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