abra2
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ABRA2
We have been using 60GB of ram for ABRA2 on deeply-sequenced bams (20,000x total, 1,200x unique, ~10 GB in compressed size). We would like to be able to realign as...
Would like to be able to pipe non-realigned sam/bam input.
Hi there! We are recently very interested in abra2 for fast and accurate reassembly/realignment of InDels. When using other tools with the realinged bam from abra2, we discovered this following...
Hi, I found the tool useful and easy to use, therefore I wanted to include it in a pipeline that I would like to make available in Mac and Linux....
Hi, I keep facing this issue when making the Makefile rm -rf target mvn clean [INFO] Scanning for projects... [INFO] [INFO] ----------------------------< abra2:abra2 >----------------------------- [INFO] Building abra 2.19 [INFO] --------------------------------[...
Thanks for the software, it has been incredibly helpful. Hopefully, this question is not a repeat and this is an appropriate place to ask this questions. I’m curious about some...
The original HashMap lookup rc on my computer takes ~280ms to reverese complement 200k strings, the new version completes the same task ~120ms with a switch statement.
I was trying out ABRA2 on a set of alignments produced by RTG, which use the = and X CIGAR operators to indicate match/mismatch instead of the generic M operator....
Hello, I run abra2.22 as part of cwl pipeline of nucleo. abra2 runs for few days and than crashed: ``` INFO Fri Sep 09 09:01:34 UTC 2022 PROCESS_REGION_MSECS: chr9_5391847_5392563 802613...
Hi there, I've encountered this recently while trying to run ABRA2-processed bams through Strelka2. Strelka2 appears to yield empty VCFs, with all variants labeled as 'non-candidate' when given ABRA2 bams....
