pufferfish
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COMBINE-lab
An efficient index for the colored, compacted, de Bruijn graph
Hi, Thanks for publishing pufferfish! I was interested in trying it for genome alignment, but when I tried to index GRCh38 it printed out a lot of warnings as if...
In many cases, I get a single FASTQ with pared end reads "interleaved", namely reads for a pair are consecutive, have the same name except for a trailing `/1` or...
Pufferfish does not "make install" fully. This is on CentOS 8. ``` package=pufferfish #from current_version.txt in download pversion=1.0.0 TOPDIR=/usr/common/modules/el8/x86_64/software/${package}/${pversion}-CentOS-vanilla THELUA=/usr/common/modules/el8/x86_64/modules/all/${package}/${pversion}-CentOS-vanilla.lua #as modules on 2020/06/09 for CentOS 8 cd /usr/common/src git...
The supplied cmake/Modules/FindJemalloc.cmake does not work on CentOS 8 even though jemalloc and jemalloc-devel are both installed from RPMs. It was replaced with the FindJeMalloc.cmake from inkscape and that did...
I'm opening this issue here because I believe it's more of a pufferfish-related matter, but will use the issue template from your salmon repository. **Is the bug primarily related to...
Output unmapped reads to FASTQ names file (like Salmon `--writeUnmappedNames` feature), alignments SAM file, or FASTQ files
The initial fixFasta step of Pufferfish indexing is single-threaded, and when there are a lot of sequences in the reference it takes a lot of time. From the outside it...
While trying to compile https://github.com/COMBINE-lab/salmon on an IBM Power system, compilation fails during the pufferfish build phase because of SSE flags passed to the compiler for constituent ksw2pp: ``` 236.4...
Hello, I tried to install pufferfish on Ubuntu 22.04.3 LTS following the guide > git clone [email protected]:COMBINE-lab/pufferfish.git > cd pufferfish > mkdir build > cd build > cmake ../ >...
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An efficient index for the colored, compacted, de Bruijn graph