Portable static build
Avoids host GLIBC/libstdc++/libgcc/zlib shared-library version problems on Linux x86-64.
SciAlign v0.2.2 Portable
Fast, strict short-read mapping in a portable Linux binary.
SciAlign is a standalone ungapped short-read aligner for Linux x86-64. It uses an FM-style reference index, whole-read or seed mismatch modes, multi-sample FASTQ input and a fully static portable build. Version 0.2.2 adds multithreaded index construction.
What it does
SciAlign workflow.
Purpose-built scientific software with downloadable documentation and reproducible local workflows.
Multithreaded indexing
Use --threads N or --threads auto to build independent complete-contig FM-index blocks concurrently.
Whole-read mode
Allow 0 to 3 substitutions across the complete end-to-end read with --whole-mm.
Seed mode
Constrain mismatches in the seed with --seed-mm plus seed-length and quality-limit controls.
Strand control
Search both orientations or restrict mapping to forward or reverse-complement orientation.
Batch FASTQ processing
Align multiple FASTQ/FASTQ.GZ samples in one run, producing one SAM per sample plus mapping_statistics.tsv.
Usage
Index and align.
Build a .sai index first, then align one or more FASTQ samples:
scialign index \ --reference reference.fa \ --save-index reference.sai \ --threads auto scialign align \ --index reference.sai \ --reads sample1.fastq.gz sample2.fastq.gz \ --results mapped --whole-mm 1 \ --strand both --threads 12
Install / launch
Start the release locally.
tar -xzf SciAlign_v0.2.2_portable_linux_x86_64.tar.gz cd SciAlign_v0.2.2_portable_linux_x86_64 chmod +x scialign* ./scialign* --help
Research-use software. SciAlign performs ungapped end-to-end alignment. Use a splice-aware/gapped aligner when introns, long indels, local clipping or complex structural variation must be modeled.