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adapters

amazon-s3-backup

bacterial_genome_analysis

Analysis pipeline for recovery of bacterial genomes (primary focus on Treponema pallidum) isolated directly from clinical material

bed2_summary

get smallRNAseq summary in piclusters, transposons and genes from bed2 files generated by piPipes or other softwares

cutadapt

cutadapt removes adapter sequences from sequencing reads

deeptools

Tools to process and analyze deep sequencing data.

dekupl-annotation

Annotate DE contigs identified by DE-kupl.

desalt

deSALT - De Bruijn graph-based Spliced Aligner for Long Transcriptome reads

fivepseq

An application for analysis of 5′ endpoints distribution in RNA sequencing datasets. This is particularly useful for techniques that capture 5′ monophosphorylated RNAs, such as 5PSeq, PARE-seq or GMUC. It may also be useful for ribosome profiling datasets and alike.The main workflow of fivepseq is intended for downstream analysis of alignment files to describe the distribution of 5′ endpoints of reads relative to translation start and stop sites, as well as relative to amino acids or codons. It also computes frame preference of 5′ endpoint distribution and captures periodicity patterns.

jacusa

JAVA framework for accurate SNV assessment

marginalign

UCSC Nanopore

mudskipper

A tool for projecting genomic alignments to transcriptomic coordinates

pipipes

piRNA pipeline collection developed in the Zamore Lab and ZLab in UMass Med School

riboseqc

Pipeline for Quality Control of Ribo-Seq data, selection of P-site offsets, and codon usage statistics.

ribowaltz

optimization of ribosome P-site positioning in ribosome profiling data

rmarkdown-notes

se-mei

Tools for finding mobile element insertions from single-end datasets

squire

Software for Quantifying Interspersed Repeat Expression

tera-seq_snakemake

Snakemake workflow for TERA-Seq data analysis

umi-tools

Tools for handling Unique Molecular Identifiers in NGS data sets

utils

Variable utils that I created or collected