Andreas Wilm's repositories
compbio-utils
miscellaneous bioinfo scripts
agrep
AGREP - approximate GREP for fast fuzzy string searching. Files are searched for a string or regular expression, with approximate matching capabilities and user-definable records. Developed 1989-1991 by Udi Manber, Sun Wu et al. at the University of Arizona. ISC open source license since Sept. 2014.
andreaswilm.github.io
Andreas Wilm's Github Pages
bamsurgeon
tools for adding mutations to existing .bam files, used for testing mutation callers
construct3
ConStruct: Construction of RNA consensus structures.
EMIRGE
EMIRGE reconstructs full length ribosomal genes from short read sequencing data.
got-your-back
Got Your Back (GYB) is a command line tool for backing up your Gmail messages to your local computer. It uses the standard IMAP protocol but also takes advantage of some custom Gmail IMAP extensions. For help with GYB, see the Getting Started Guide at https://github.com/jay0lee/got-your-back/wiki
graphmap
GraphMap - A highly sensitive and accurate mapper for long, error-prone reads
ICGC-TCGA-DREAM-Mutation-Calling-challenge-tools
Tools for participants in the ICGC-TCGA DREAM Mutation Calling challenge
nextflow
A DSL for data-driven computational pipelines
pysam
Pysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.
sandbox
my sandbox
scRNApipe
Single Cell RNAseq pipeline readtransforming using umis, alignment, gene-deduplication by umi-tools and counting
split_bam
Splits your BAM/SAM stream into one file per region given in bed file
split_bam_by_chr
Split BAM/SAM by chromosome
transmogrify.htmltesting
utils and transmogrifier blueprints for testing
umis
Tools for processing UMI RNA-tag data