========================================================== aLib: a sequencing pipeline for ancient and modern DNA
aLib is:
- an open-source set of modules to process ancient and modern DNA data from raw intensities to usable BAM files
- It is aimed at mid-size sequencing centers processing ancient DNA using Illumina sequencers
- It performs basic processing that should be common to any sequencing pipeline.
- It features:
- Online monitoring interface for sequencing runs
- Online form with analysis requirements
- Basecalling either with freeIbis or using the default basecaller Bustard
- Trimming of sequencing adapters, merging of partially overlapping mate-pairs and flagging of chimeric sequences
- Demultiplexing based on read group assignment quality
- Basic filtering
- Basic Quality control
To install:
Installation instructions are provided on the wiki: