fg6

n50

C++ code to evaluate basic stats for a fasta/fastq(.gz) file

YeastStrainsStudy

Scripts to download the PacBio, ONT and MiSeq datasets used in https://www.nature.com/articles/s41598-017-03996-z and run the pipelines as described in the paper or simply download the final assemblies as generated by the authors.

EBI_NGS_Assembly

Practical exercises for the EBI NGS Course -- Assembly

smis

SMIS: Single Molecular Integrative Scaffolding

cutshorts

fg6.github.io

My Personal Page

forACT

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

fq2fa

random_subreads

Subsample reads from a fastq/fasta file to a desired read depth. Choose random selection or new mean read length

seq_factotum

A package for fast genomic sequences manipulation or interrogation

hicclus

HI-C data Analysis -- In active development --

hicfilter

Filtering the scaffold links that comes from the same chromosomes from HiC reads with a Random Forest/XGboost model

MachineLearning

Machine Learning projects and tests

MECAT

MECAT: an ultra-fast mapping, error correction and de novo assembly tool for single-molecule sequencing reads

selfastq

Select reads in a fastq according to predetermined list

shredPilon

Pipeline to run Pilon on a draft assembly in parallel chunks

test_ml

progetto di prova

Tutorials

A list of tutorials and how-tos for data analysis and data science