Create assembly from BAC short read sequences

One step pipeline to clean, filter and assemble short reads into a contiguous bac sequence.

• SGE cluster
• python 2.xx
• seqtk(https://github.com/lh3/seqtk) (cleaning bases and adapters)
• bwa mem(https://github.com/lh3/bwa) (to map reads on vector contaminents)
• SPAdes(http://bioinf.spbau.ru/spades) (assembler)

One needs to edit back2ass.sh in order to edit path of the different dependencies. So far, the script assumes that you are a CBGP cluster user at INRA, so path are good for you. Otherwise, well, change them :)

• Two paired fastq file (can be gz compressed)
• A fasta file with the vector and possible contaminent sequences

qsub back2ass.sh Forward.fastq Reverse.fastq vector.fasta qual

see intput to make a guess on fastq and fasta origin. qual is a floating number use as a threshold when cleaning fastq files for bases accuracy (ex 0.01). see seqtk manual for additional informations.

• Various intermediary files in a tmp directory
• mapping results in a dedicated directory
• assembly results in a dedicated directory