AncesBin v1.0

Pipeline to bin 10X, HiC, PacBio and ONT reads based on ancestry assemblies.

Download and Compile:

Requirements for compiling: gcc:

$ git clone  https://github.com/wtsi-hpag/AncesBin.git 
$ cd AncesBin 
$ ./install.sh

If everything compiled successfully you must see the final comment: "Congrats: installation successful!"

External packages

The genome aligner BWA (http://bio-bwa.sourceforge.net) and SMALT (http://www.sanger.ac.uk/science/tools/smalt-0) are downloaded and compiled by AncesBin.

There are three codes bin10x, binHiC and binLong in the package

Run bin10x:

       $ /full/path/to/AncesBin/src/bin10x -nodes <nodes> Input_sorted_bam Input_data_file Output_directory \

       Parameters:
         nodes:            number of CPUs requested  [ default = 30 ]
         Input_sorted_bam: read name sorted longranger BAM file
                           input a bam file which had been produced by using lariat in longranger, 
                    (a). rename the assembly file:
                     $ /full/path/to/AncesBin/src/scaff-bin/seqbin_rename -name MAT MAT_assembly.fa MAT_ref.fasta 
                     $ /full/path/to/AncesBin/src/scaff-bin/seqbin_rename -name PAT PAT_assembly.fa PAT_ref.fasta

		(b). cat assemblies
                     $ cat MAT_ref.fasta PAT_ref.fasta > MPAT_ref.fasta

		(b). generate reference assembly file using longranger
		 $ longranger mkref MPAT_ref.fasta 

		(c). align 10x reads using lariat longranger
		 $ longranger align --fastq="reads_10x" --sample=fTakRub1 --reference="refdata-MPAT_ref" --localcores=50 --id=10x-align 
		 Note: for reads_10x please provide full path
                           10x-align is an output directory

                    (d). sort the longranger bam
                     $ samtools sort -n -@ 30 -O BAM -o possorted_sort.bam possorted_bam.bam 

         Input_data_file:  a text file to point the locations of the reads in paired files\n");

q1=/lustre/scratch116/vr/projects/Tes1_S1_L008_R1_001.fastq.gz
q2=/lustre/scratch116/vr/projects/Tes1_S1_L008_R2_001.fastq.gz
q1=/lustre/scratch116/vr/projects/Tes1_S2_L008_R1_001.fastq.gz
q2=/lustre/scratch116/vr/projects/Tes1_S2_L008_R2_001.fastq.gz
q1=/lustre/scratch116/vr/projects/Tes1_S3_L008_R1_001.fastq.gz
q2=/lustre/scratch116/vr/projects/Tes1_S3_L008_R2_001.fastq.gz
q1=/lustre/scratch116/vr/projects/Tes1_S4_L008_R1_001.fastq.gz
q2=/lustre/scratch116/vr/projects/Tes1_S4_L008_R2_001.fastq.gz \

         Output_directory: a director contained all the binned 10X reads\n");

Run binHiC:

   $ /full/path/to/AncesBin/src/binHiC -nodes 30 MAT_ref.fasta PAT_ref.fasta Input_read_1.fq.gz Input_read_2.fq.gz Output_head  \

       Parameters:
         nodes:              number of CPUs requested  [ default = 30 ]
         MAT_ref.fasta:      ancestry MAT assembly 
         PAT_ref.fasta:      ancestry PAT assembly 
         Input_read_1.fq.gz: gzipped HiC read 1 
         Input_read_2.fq.gz: gzipped HiC read 2
         Output_head:        output 4 files as Output_head_1.MAT.gz Output_head_2.MAT.gz Output_head_1.PAT.gz Output_head_2.PAT.gz

Run binLong:

   $ /full/path/to/AncesBin/src/binLong -nodes 30 MAT_ref.fasta PAT_ref.fasta Input_data_file Output_directory  \

       Parameters:
         nodes:            number of CPUs requested  [ default = 30 ]
         MAT_ref.fasta:    ancestry MAT assembly 
         PAT_ref.fasta:    ancestry PAT assembly 
         Input_data_file:  a text file to point the locations of the reads in gzipped files\n");

/lustre/fTakRub1/PacBio/fasta/m54097_180320_123755.subreads.fasta.gz
/lustre/fTakRub1/PacBio/fasta/m54097_180321_135512.subreads.fasta.gz
/lustre/fTakRub1/PacBio/fasta/m54097_180322_133901.subreads.fasta.gz
/lustre/fTakRub1/PacBio/fasta/m54097_180323_154627.subreads.fasta.gz \

         Output_directory: a director contained all the binned PacBio or ONT long reads\n");