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bcftools

This is the official development repository for BCFtools. To compile, the develop branch of htslib is needed: git clone --branch=develop git://github.com/samtools/htslib.git htslib

beast-mcmc

Bayesian Evolutionary Analysis Sampling Trees

bedtools2

A powerful toolset for genome arithmetic.

chromeister

A dotplot generator for large chromosomes

cmast-genome-assembly

Methods and tools used for assembling the C. mast RC genome

covid-19-us

Covid-19 reported cases data and analysis for US states - Last Update : April 7, 2020

delly

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

disir_package

ligand receptor cell to cell

exampledatasets

additional example files for cytoscape, gephi and neo4j

fastqc

A quality control analysis tool for high throughput sequencing data

gatk

Official code repository for GATK versions 4 and up

hifiadapterfilt

Remove CCS reads with remnant PacBio adapter sequences and convert outputs to a compressed .fastq (.fastq.gz).

htseq

HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.

irfinder

Detecting intron retention from RNA-Seq experiments

isoseq

IsoSeq3 - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads

li-bioinformatics

General scripts/code/pipeline for use with downstream analysis of large scale data

mirdeep2

Discovering known and novel miRNAs from small RNA sequencing data

molbiocloud

msisensor

microsatellite instability detection using paired tumor-normal

palmo

Identify Intra-, Inter-donor variations in bulk or single cell longitudinal dataset

picard

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

subset-bam

tcrmatch

telseq

A software for calculating telomere length

trinityrnaseq

Trinity RNA-Seq de novo transcriptome assembly

vcftools

A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.

visiumtrim

TSO and polyA trimming of fastq files generated with 10x Visium