HTStream
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s4hts
A high throughput sequence read toolset using a streaming approach facilitated by Linux pipes
Command to Verify ``` valgrind --leak-check=full \ --show-leak-kinds=all \ --track-origins=yes \ --verbose \ ./hts_SuperDeduper/hts_SuperDeduper -T ../regression/hts_SuperDeduper.tab6 ``` Output from Valgrind ``` ==44234== HEAP SUMMARY: ==44234== in use at exit: 472...
Hello, I am trying to use HTStream. I have based my code off the tutorial here: https://ucdavis-bioinformatics-training.github.io/2020-mRNA_Seq_Workshop/data_reduction/01-preproc_htstream_mm and I referred to the sbatch example script heavily: ``` #!/bin/bash #SBATCH --job-name=htstream...
**Describe the bug** Heya, thanks for maintaining HTStream :) For the attached example files, the number of hits identified by hts_SeqScreener vary depending on whether the forward reads or reverse...
**Describe the bug** hts_AdapterTrimmer and hts_PolyATTrim did not remove adapters in some reads that have incomplete, degeneracy or extra sequence in the adapter sequence of the 3' end of the...
Need to trim 2 libraries/run to the same length, can be variable cut, can do so now by specifying CutTrim early with a specific trim, however 1 library has to...
https://s4hts.github.io/HTStream/ needs to be updated with a section for hts_LengthFilter.
I use the CMAKE_PREFIX_PATH option in cmake to install htstream into a non-default directory, but when I run "make install" it still tries to install the binaries in /usr/local/bin. Also,...
**Is your feature request related to a problem? Please describe.** Principle of each app should do one thing and one thing well, is violated with this optoins **Describe the solution...
hts_SeqScreener is meant to filter/identify reads originating from specific source sequences (PhiX as default, but also ribosomal sequences or adapters etc). **Is your enhancement request related to a problem? Please...
"Paired_end": { "in": 59766627, "out": 59766627, "discarded": 0, "Read1": { "basepairs_in": 2305056164, "basepairs_out": 2306023101, "leftTrim": 1887576, "rightTrim": 18446744073706697103.