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actc

Align subreads to ccs reads

agp_fail

Does your FASTA match your AGP?

alignreadtohaphmm

bampals

an assortment of methods for bam|sam|cram files

bevel

Working toward a probabilistic MSA tool

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)

coverup

sv-popgen

daligner

Find all significant local alignments between reads

dasvc

De-novo Assembly Structural Variant Caller

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

fastqi

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++

mcutils

mergesvcallers

heuristics to merge structural variant calls in VCF format.

minimap

Experimental tool to find approximate mapping positions between long sequences

pbbioconda

PacBio Secondary Analysis Tools on Bioconda

pooled-mapping

A description of the Tetrahymena pipeline used to map a recessive mutant

popfastaaa

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

samtools

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

skera

SKERA

smartie-sv

calling SVs from Blasr contig level alignments

snakepit

useful snakemake recipes - mostly cluster based

triobinning

Scripts for manually classifying reads and make figures