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:

https://github.com/grenaud/aLib/wiki