creates a list of accessible sites following suggestions in Ag1000g by leveraging files produced by bedtools genomeCov and bam files
creates a circos formatted file from nucmer output of genome alignments
converts a PSL file from HAL tools to liftover.table file
removes duplicates, paralogs, from liftover.table produced by hal
reorients a vcf file to coordinates of an aligned reference
fast deinterleave fastq files
opposite of deinterleave on fastq files
Iterative error correction with sga-ice version which does not store tmp files and fills your drive
iterative run of w2rap for testing different kmers
calculate basic set of metrics from a genome assembly fasta. Author: Keith Bradnam, Genome Center, UC Davis
filtering on de novo assemblies using blast and nucmer against known species genomes
simple stupid script to size select on a fasta file using an index. It is hard coded so probably just use seqtk instead.
Provides a bed file of location of gaps and hist of the size distribution. Author Linnéa Smeds 19 oct 2010
I made this script to create a consensus between 2 de novo genome assemblies each from a difference individual but from the same species. The de novo assemblies were then scaffolded in ragout. N's in 1 scaffolded assembly were somtimes present as sequence in the other. If you align the 2 genomes with Mauve to product a xmfa, you can then produce a consensus with fewer gaps than either alone
creates a single consensus genotype in a VCF from multiple outgroups. usage to detect polarize conflicts among outgroups and when programs only allow for a single sample to be designated as outgroup.