SimSeq
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jstjohn
An illumina paired-end and mate-pair short read simulator. This project attempts to model as many of the quirks that exist in Illumina data as possible. Some of these quirks include the potential for...
Hello, Thanks for the design of this useful tool! I would provide a little suggestion that the read count generated can be set by an optional way: a new parameter...
Hi I hope you are still checking here :) `java -jar SimSeq.jar -1 100 -2 100 --error SimSeq-master/examples/hiseq_mito_default_bwa_mapping_mq10_1.txt --error2 SimSeq-master/examples/hiseq_mito_default_bwa_mapping_mq10_2.txt --insert_size 2000 --insert_stdev 200 --mate_pair --mate_frag 500 --mate_frag_stdev 50 --mate_pulldown_error_p...
Trying to make the getErrorProfile tool. Getting the following when I run `make` ``` miniconda2/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: getErrorProfile.o: in function `getErrorProfile': getErrorProfile.c:(.text+0x5b3): undefined reference to `phred33ToPhred' miniconda2/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: getErrorProfile.c:(.text+0x5d9): undefined reference to `phred64ToPhred'...
Hi John, I recently read the Assemblathon 1 paper published in Genome Research and may be interested in using SimSeq for a project I am working on. In the paper,...
I compile the getErrorProfile.c and it throwed the following error: ``` gcc -I../ThirdParty/kent/inc -I../inc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -lm getErrorProfile.o ../ThirdParty/kent/lib/common.o ../ThirdParty/kent/lib/dlist.o ../ThirdParty/kent/lib/bPlusTree.o ../ThirdParty/kent/lib/dystring.o ../ThirdParty/kent/lib/linefile.o ../ThirdParty/kent/lib/nib.o ../ThirdParty/kent/lib/sqlNum.o ../ThirdParty/kent/lib/base64.o ../ThirdParty/kent/lib/dnaLoad.o ../ThirdParty/kent/lib/errabort.o...
Hello, just a minor comment, the read number argument (-n,--read_number) seems to be for fragment number, thus twice the amount of reads are generated. Maybe change the option name to...
Hello, I have now proceeded to the synthetic read generation itself. However, when checking my alignment with 'samtools tview', the reads present approximately 30 mismatches each, for a total of...
