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fastdna

faster_lmm_d

A faster lmm for GWAS. Supports GPU backend.

fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting...)

fastq-pair

Match up paired end fastq files quickly and efficiently.

fastq_stat

Statistic illumina Fastq file

fastqseqstats

calculate base frequency and quality distribution from FASTQ file

fastquick

Ultra Fast NGS Data QC Tool

faststructure

A variational framework for inferring population structure from SNP genotype data.

fermikit

De novo assembly based variant calling pipeline for Illumina short reads

fgwas

Functional genomics and genome-wide association studies

figtree

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

filterfasta

FASTA file parser to extract or pipeline amino acid sequences.

find-motif

Program to extract small nucleotide motifs from Genome sequences

find_circ

tools to find circRNAs in RNA-seq data

finding-a-gene-in-a-strand-of-dna

An important problem genomics scientists encounter regularly: how to identify genes in a strand of DNA. To tackle this problem, we need to understand strings: series of characters such as letters, digits, punctuation, etc. A gene for a protein has a start codon, followed by a substring that is a multiple of 3, followed by a stop codon.

findingori

Finding origin and terminus of replication in bacterial chromosomes

findorf

Find open reading frames in a DNA FASTA file.

firebrowser

An R client for broads firehose pipeline, providing TCGA data sets

fishertestforgenomicoverlapsmilospjanicmod

Combined bash/R script performs specialized Fisher's exact test and generates p-value that shows significance for the overlap of two sets of genomic regions. Statistical test includes genomic background i.e. combined ENCODE set of open chromatin regions to calculate constituents of the Fisher exact test contingency matrix.

fiveminutestats

A repo of short "vignettes" illustrating statistical concepts; http://stephens999.github.io/fiveMinuteStats/analysis/

flashpca

Fast Principal Component Analysis of Large-Scale Genome-Wide Data

flexaid

Flexible Artificial Intelligence Docking

flexidot

Highly customizable, ambiguity-aware dotplots for visual sequence analyses

flip

Flip - translates and reformats DNA sequences

flu_analysis_pipeline

flute

Agent-based influenza epidemic model

fm-pipeline

FineMapping pipeline using GWAS summary statistics

fmap

Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies

focus

A model to identify organisms present in metagenomes in seconds

foract

Pipeline to prepare alignments for visualization with ACT (goo.gl/1T28jX) and for locating possible inter-chromosomal re-arrengments/misjoints