zeeev

wham

Structural variant detection and association testing

smartie-sv

calling SVs from Blasr contig level alignments

mergeSVcallers

heuristics to merge structural variant calls in VCF format.

vcflib

a simple C++ library for parsing and manipulating VCF files, + many command-line utilities

DASVC

De-novo Assembly Structural Variant Caller

minimap

Experimental tool to find approximate mapping positions between long sequences

bamPals

an assortment of methods for bam|sam|cram files

bevel

Working toward a probabilistic MSA tool

zk_tools

my bioinformatics code

snakePit

useful snakemake recipes - mostly cluster based

popFastaaa

Simple stand-alone programs for analysis of aligned Multi-FASTA formated files.

fastqi

mcutils

samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

actc

Align subreads to ccs reads

AGP_FAIL

Does your FASTA match your AGP?

bioconda-recipes

Conda recipes for the bioconda channel.

BitVector

BitVector Implementation in Nim

bloom

Automatically exported from code.google.com/p/bloom

ccs

CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)

DALIGNER

Find all significant local alignments between reads

dow

day of the week ^DJI analysis

FALCON-Phase

FALCON-Phase integrates PacBio long-read assemblies with Phase Genomics Hi-C data to create phased, diploid, chromosome-scale scaffolds

Flye

Fast and accurate de novo assembler for single molecule sequencing reads

GenericStack

Generic Stack in C

KDTree

A KD-Tree designed for chaining DNA alignments

libgff

A simple GFF/GTF parsing library in C++

pbbioconda

PacBio Secondary Analysis Tools on Bioconda

skera

SKERA

TrioBinning

Scripts for manually classifying reads and make figures