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jts
de novo sequence assembler using string graphs
Hello, I have tried to run sga-bam2de.pl a few times with bowtie sorted bam files. I changed the samtools bit by adding -o and .bam at the end to make...
Hi, there seem to be an issue on line 70 when compiled with C++14 (either clang or gcc), ``` bool good = getline(*m_pReader, line); ``` which reports ``` error: no...
I'm merely the installer of SGA on a shared HPC resource, but I wanted to say thanks for providing some examples so that an installation can be tested out, ahead...
Hello! I know that SPADES gives the depth of coverage of each contig in contigs' headers, but I do not know how to get this information in SGA, could anyone...
Enhancement as per Twitter discussion: https://twitter.com/macmanes/status/655917967884980224 Allow corrected reads to be sent to the stdout. There might be several other places where this could save a lot of time. For...
Compiler diagnosis should be clear: ``` ./InverseSuffixArray.h:10:9: warning: 'INVERSESUFFIXARRAY_H' is used as a header guard here, followed by #define of a different macro [-Wheader-guard] #ifndef INVERSESUFFIXARRAY_H ^~~~~~~~~~~~~~~~~~~~ ./InverseSuffixArray.h:11:9: note: 'INVERSESUFFIXARRAH_H'...
It seems you forget to delete the qual when you delete a base pair at error correcting, which make read length and qual length different. For example: after error correcting...
Because the git Issue tracker does not support compressed files, I have attached relevant FASTA file in the SGA google user group. I wrongly posted an old version of code...
Hello! I address you because I want to perform a little experiment using graphs. I would like to make a string graph from several similar reference genomes. Once made, I...
