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jts
de novo sequence assembler using string graphs
The default value shown in help is 150bp but in reality it's 300bp https://github.com/jts/sga/blob/229293b2c97777aa015581b6075ed6b60050b34d/src/SGA/assemble.cpp#L73
Hello everyone I am getting some truble with SGA installation cause of google-sparsehash. I have downloaded it from this link (https://anaconda.org/bioconda/google-sparsehash/files), then at SGA folder i write `./configure --with-sparsehash=../../google-sparsehash/ --with-bamtools=/opt/bamtools`...
Hi, I am trying to run age-preqc-report.py. However, it was not included in the condo sga installation so I had to download it from GitHub. It recognizes my output from...
Hello Jared, After ran “preprocess”, “correct”, "filter", "overlap" and “assemble” with default settings, I got two contigs files for reference genome ref_contigs.fa and query genome query_contigs.fa. When I tried to...
For me configure does not detect sparsehash-2.0.3 not even with current git master at commit af73db617738ff3e4c85cb370f485b208d6be15c : ``` ./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-dependency-tracking --disable-silent-rules --libdir=/usr/lib64...
Hi, In overlap.cpp, the OverlapProcess.h is included but I don't seem to find it in the source code. Do you know where I could find it?
Cloned today and found two issues with 'configure': File 'configure' line 5879 does not specify a path for the bamtools file 'api/BamReader.h', so it will never be able to figure...
I am trying to index a large .fastq file (~700GB) by `nohup sga index -a ropebwt --no-reverse -t 6 -vvv TT2.fastq &`, however, the job in the server disappeared suddenly...
In one of my experiments involving the assembly graph, I noted that `ED read2 read1 0 46 50 3 49 50 0 0` lines are not tab-delimited. Only the ED...
What's the plan for `src/bin/{sga-align, sga-astat.py, sga-joinedpe, src/bin/sga-preqc-report.py}`?
