seqan / anise_basil

Methods for the detection and assembly of novel sequence in high-throughput sequencing data

SeqAn - The Library for Sequence Analysis

NOTE SeqAn3 is out and hosted in a different repository
We recommend using SeqAn3 for new applications.

What Is SeqAn?

SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. Our library applies a unique generic design that guarantees high performance, generality, extensibility, and integration with other libraries. SeqAn is easy to use and simplifies the development of new software tools with a minimal loss of performance.

License

The SeqAn library itself, the tests and demos are licensed under the very permissive 3-clause BSD License. The licenses for the applications themselves can be found in the LICENSE files.

Prerequisites

Older compiler versions might work but are neither supported nor tested.

Linux, macOS, FreeBSD

• GCC ≥ 11
• Clang/LLVM ≥ 15
• Intel oneAPI C++ Compiler 2024.0.2 (IntelLLVM)

Windows

• Visual C++ ≥ 17.0 / Visual Studio ≥ 2022

Architecture support

• Intel/AMD platforms, including optimisations for modern instruction sets (POPCNT, SSE4, AVX2, AVX512)
• All Debian release architectures supported, including most ARM and all PowerPC platforms.

Build system

• To build tests, demos, and official SeqAn applications you also need CMake ≥ 3.12.

Some official applications might have additional requirements or only work on a subset of platforms.

Documentation Resources

• Getting Started
• Manual
• Tutorial
• How-Tos
• API Documentation (stable)

Contact

• Mailing List
• GitHub Project (issues, source code)

anise_basil's Issues

make error

I tried to install anise_basil according to the readme, but the make command fails due to seqan files not being found.
Here is a log file: build_anise_basil.txt

bad_alloc

Hello, I'm trying to use anise_basil to assemble some breakpoints around a duplication. I generated a basil.vcf file and am trying to run the anise step where I get the following error after it assembles 8/123 of the sites:

00:11/00:02:49]terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc

When I run it with the -v option, I get this error description:
Building Consensus...
Building alignment graph

fragments: 0

seqs: 295

progressive alignment...
build AG..
AG
numVertices = 295
numEdges = 0
componentLength.size() = 295
numComponents = 295
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
Aborted (core dumped)

I'm running it on a small (6 Mb) section of chr2, and the basil step detects 124 potential breakpoints, all of which I use in the anise assembly.
The machine I'm running it on has 16G, and anise seems to be using only a little over 1G, so it doesn't seem to be running out of memory.

Please let me know if you would like me to send my input files.

Thanks!

New release request

I was taking the liberty to create a conda recipe for anise_basil so that I could create a galaxy tool wrapper for basil. I use basil in a prokaryotic variant pipeline that I'm trying to turn into a galaxy workflow.

Anyway, it appears that there have been some significant changes since the last release that I wanted for the galaxy tool wrapper. I was able to use a regular revision hash to move forward, but a new release would be ideal. Do you think you could create one?

Also, a colleague pointed out that the license is a BSD3 license. (I don't work with licenses enough to recognize them by content.) I was thinking that it might be nice if the license was labeled as BSD3 in some way for numbskulls like me to know which type of license it is. :P Bioconda requires the license type in their config file and I didn't know what to put.

basil test fails due to ref.fa path

The test script for basil appears to compare the vcf files without accounting for a different value for the reference path:

diff /Users/rleach/local/miniconda3/conda-bld/anise_basil_1545249514348/work/test/01/basil.vcf /var/folders/8d/z84mms353qb2n0r3n2jhww0m0000gq/T/tmp.z7rXj0Zi/basil.vcf
3c3
< ##reference=/home/manuel/Development/anise_basil/test/01/ref.fa
---
> ##reference=/Users/rleach/local/miniconda3/conda-bld/anise_basil_1545249514348/work/test/01/ref.fa

anise Segmentation fault

Basil found a very good candidate for our anticipated 2kb insert, but when I ran anise to assemble it, I get a segfault fairly quickly:

./anise_basil/build/bin/anise -ir Pseudomonas_aeruginosa_UCBPP-PA14_109.fa -im PA14_1_pe_trimmed.bam -iv PA14_1_pe_trimmed.basil.filtered.vcf -of PA14_1_pe_trimmed.basil.filtered.anise.vcf.fa
Parsing command line...
Loading global state...
Checking input...
Estimating library size...
  estimation complete |################################################| 100000/100000 [00:00:00/00:00:00]
  library size: median=344, stdDev=97.9034
Perform preparation step...
  extracted sites |                                                | 0/1 [00:00:06/00:00:00]Segmentation fault

I am using an index created by samtools:

samtools faidx Pseudomonas_aeruginosa_UCBPP-PA14_109.fa

Could that be the issue?

Thanks,
Rob