alntools processes next-generation sequencing read alignments into a sparse compressed incidence matrix (aka Equivalence Classes) and stores it in a pre-defined binary format for efficient downstream analyses and storage. It enables us to compare, contrast, or combine the results of different alignment strategies.
- Free software: Apache Software License 2.0
- Documentation: https://churchill-lab.github.io/alntools/
splitdivides a large bam file into smaller ones
bam2ecpreprocesses a bam file into binary equivalence class (EC) format
bam2emasepreprocesses a bam file into EMASE format
ec2emaseconverts binary EC file into EMASE format
emase2ecconverts EMASE format into binary EC format
rangefinds effective lengths of target sequences from alignment data
We are planning to add more features for preprocessing different formats of NGS read alignments at the population level and summarizing useful information from them. Stay tuned!