Splits a fasta file in chunks for input to mercator annotation system.
Corrects errors in mercator mapping.
Calculates median gene expression value from a gene x sample matrix.
Reads a fasta file and outputs a BED file of the undetermined (N) regions
Demultiplex illumina data.
demultiplex.py samples.txt read_1.fastq read_2.fastq read_3.fastq
The samples file is a tab delimited file with two columns. The first one corresponds to the output file name; the second corresponds to the tag sequence.
Filter FASTQ files using seq_crumbs and trimmomatic
Convert a SAM file to BAM, sort the BAM file and index it.
Basic QC of a bam file using Picard tools
Calculate the genome coverage from a BAM file
Calculate average coverage and coverage at different read depths with bedtools
Preprocess bam for variant calling (realignment + base recalibration)
Calls variants with Unified Genotypes. Supports multi-sample calling.