NextGenMap
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NextGenMap is a flexible highly sensitive short read mapping tool that handles much higher mismatch rates than comparable algorithms while still outperforming them in terms of runtime. This allows ana...
Hello, I really need help! I mapped paired-end short reads to a fasta file using ngm and piped the output to samtools. I used samtools sort to generate a sorted...
. I am using v0.5.5, and originally submitted with the following cmd: ``` ngm \ -r KN99_genome_fungidb.fasta \ -q run_1272_s_3_withindex_sequence_AAATGCA.fastq.gz \ --threads 2 \ --bam ``` but, I received this...
Hi, I have sequencing data from different lanes/batches that I've merged into a single unaligned BAM. The headers in the merged unaligned bams look something like this: ``` @RG ID:L001...
Hi there~ I wanna report an Error occurs when try to run NGM with Docker. While it can be ran through smoothly with NextGenMap installed in PC. Thank you so...
Hi, I was attempting to re-align reads that were aligned with another aligner. I was using the `--keep-tags` option, primarily because I have RG tags and OQ tags that I...
Hello, There is any option to set the orientation of the mates reads? Thanks Amit
This is a proposed fix for #34: * Use std::thread::hardware_concurrency() to find the available cores and use this number as `num_devices` parameter when calling `clCreateSubDevices()` instead of 256. * Add...
Hello, I was tying NGM at Texas Advanced Computing Center (https://portal.tacc.utexas.edu/user-guides/stampede2). However, an error occurs constantly. I compiled the NGM through CMake. I wonder if anyone has insight on how...
After successful compilation, the `ngm` script is installed with incorrect permissions under `/usr/bin`: ``` $ ls -l /usr/bin | grep ngm -rwxr-x---. 1 root root 466 May 23 14:16 ngm...
