bascet 0.4.0

Bascet is a tool to preprocess single-cell data, handling barcode detection, trimming, QC, and managing the execution of custom tools for each cell
Documentation 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69


pub mod getraw;
pub mod mapcell;
pub mod shardify;
pub mod transform;
pub mod featurise_kmc;
pub mod query_kmc;
pub mod query_fq;
pub mod bam2fragments;
pub mod kraken;
pub mod snpcall;
pub mod countchrom;
pub mod countfeature;
pub mod sam_add_barcode_tag_cmd;
pub mod minhash_hist;
pub mod threadcount;
pub mod extract;
pub mod extract_terminal;
pub mod countsketch_mat;

pub use extract_terminal::ExtractStreamCMD;

pub use query_kmc::QueryKmcCMD;
pub use query_kmc::QueryKmc;
pub use query_kmc::QueryKmcParams;

pub use query_fq::QueryFqCMD;
pub use query_fq::QueryFq;

pub use featurise_kmc::FeaturiseKmcCMD;
pub use featurise_kmc::FeaturiseKMC;
pub use featurise_kmc::FeaturiseParamsKMC;

pub use minhash_hist::MinhashHistCMD;
pub use minhash_hist::MinhashHist;

pub use mapcell::MapCellCMD;
pub use mapcell::MapCell;

pub use getraw::GetRawCMD;
pub use getraw::GetRaw;

pub use shardify::ShardifyCMD;
pub use shardify::Shardify;

pub use transform::TransformCMD;
pub use transform::TransformFile;

pub use bam2fragments::Bam2FragmentsCMD;
pub use bam2fragments::Bam2Fragments;

pub use kraken::KrakenCMD;

pub use countchrom::CountChromCMD;
pub use countchrom::CountChrom;

pub use countfeature::CountFeatureCMD;
pub use countfeature::CountFeature;

pub use sam_add_barcode_tag_cmd::PipeSamAddTagsCMD;



pub use extract::ExtractCMD;


pub use threadcount::determine_thread_counts_1;
pub use threadcount::determine_thread_counts_2;
pub use threadcount::determine_thread_counts_3;