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chip-seq-pipline

This is a general pipeline to analyze CHIP-Seq data

circu_check

Scripts to check contig circularity

fastp

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

fastq_2_fasta

gb_taxonomy_tools

GenBank taxonomy processing tools

ggpubr

'ggplot2' Based Publication Ready Plots

ggupset

Combination matrix axis for 'ggplot2' to create 'UpSet' plots

gintools

[Dev] Tools for genomic DNA integration analysis

grabseqs

Bulk download all reads from an SRA project

hisss

Snakemake workflow to download and/or align reads to targets and produce useful outputs.

igram.ecoli.strains

ivirp

Integrative virome pipeline

liang2019

Step-wise assembly of the neonatal virome modulated by breast feeding.

liang2019veo

The dynamics of the stool virome in very early onset inflammatory bowel disease

mgv

Supporting code for uncultivated gut virus manuscript

microrna-pipline

multifastats

Multifastats: Multi-Fasta Sequence Stats. Free python-based program that, from a set of a set of 'fasta' sequences (as group or individually), produces basic outputs and statistics (N50, %GC, molecular weight, cut in kmers and concatenate sequences using defined spacers). And also allows to apply some filters and select subgroups by length and/or type. This runs in Windows, Linux and Mac OS.

peppan

Phylogeny Enhanded Prediction of PAN-genome

public

rna-seq-alternative-splicing-analysis

rna-seq-differentially-expression-analysis

sbx_bowtie2_mapping

sbx_cdhit

sbx_dedup

Sunbeam extension

sortmerna

SortMeRNA: next-generation sequence filtering and alignment tool

sunbeam_neutrino

Downstream analysis after using sunbeam pipeline.