nextsv

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Can I use nextsv for ultra-long nanopore data?

1

Can I use nextsv for ultra-long nanopore data?

yweii

hello li, I read your review paper "A survey of algorithms for the detection of genomic structural variants from long-read sequencing data" and found NextSV is a pipline that ensemble...

hhy18

NextSV3 can't install

1

I'm installing NextSV3, but I'm encountering some errors： I have installed these minimap2 =2.22 CuteSV=2.0.1 samtools=1.9 gcc=4.8.2 sniffles=2.0.7 My Syetem: Ubuntu 18 I have cloned the repository using "git clone...

weriss

NextSV No Output

33

After successfully running the python command to get the output directory and work.sh, I ran the work.sh file. However, I got this output. running script 1 input file(s): output prefix:...

543090lee

``` Traceback (most recent call last): File "/data/Softwares/nextsv/nextsv2.py", line 554, in main() File "/data/Softwares/nextsv/nextsv2.py", line 128, in main check_samtools_version(settings) File "/data/Softwares/nextsv/nextsv2.py", line 254, in check_samtools_version RuntimeError: command '/home/.conda/envs/nextsv/bin/samtools sort' return...

LYC-vio

Hi, I'm trying to run NextSV on several datasets, however, some of them only provide the fasta format. Is it possible to run NextSV on fasta files? Thank you

LYC-vio

unclear NextSV issues

2

I am running NextSV2 and I get these issues in the log files: Traceback (most recent call last): File "/BiO/Access/home/bioapps/nextsv/nextsv2.py", line 553, in main() File "/BiO/Access/home/bioapps/nextsv/nextsv2.py", line 128, in main...

astulaaa

`GLIBCXX_3.4.20' not found

5

I'm trying to use NextSV2 to identify SV using Nanopore data, specifically using the sniffles caller. I've installed Sniffles and can run it as a stand alone caller with no...

wlaw13