Spades assembly pipeline

Contents

spades-prep.sh:

Preprocesses reads and aligns them to the indicated reference with BWA.

spades-assembly.sh

Runs SPAdes de novo assembly and QUAST, orienting contigs to a reference sequence.

Requirements:

• GNU parallel
• pipe-trim17-replaceDots.py (included)
• sickle
• bwa mem
• samtools
• QUAST
• SPAdes
• filter_contigs.py (included)

Configuration:

• Index human genome .fasta with bwa and specify path in spades-prep.sh.
• Specify path of reference sequence in spades-assembly.sh
• Specify path of annotation file in spades-assembly.sh
• Make sure all the scripts listed above are on PATH

The directory testing contains a test dataset.