bio-0.5.2: A bioinformatics library

Safe Haskell | Safe-Inferred

Bio.Sequence.SFF_filters

Contents

- Discarding filters
- Trimming filters
- Utility functions
- Data

Description

This implements a number of filters used in the Titanium pipeline, based on published documentation.

Synopsis

- type DiscardFilter = ReadBlock -> Bool
- discard_empty :: DiscardFilter
- discard_key :: String -> DiscardFilter
- discard_dots :: Double -> DiscardFilter
- discard_mixed :: DiscardFilter
- discard_length :: Int -> DiscardFilter
- type TrimFilter = ReadBlock -> ReadBlock
- trim_sigint :: TrimFilter
- sigint :: ReadBlock -> Int
- trim_primer :: String -> TrimFilter
- find_primer :: String -> ReadBlock -> Int
- trim_qual20 :: Int -> TrimFilter
- qual20 :: Int -> ReadBlock -> Int
- dlength :: [a] -> Double
- avg :: Integral a => [a] -> Double
- clipFlows :: ReadBlock -> Int -> ReadBlock
- clipSeq :: ReadBlock -> Int -> ReadBlock
- flx_linker :: [Char]
- ti_linker :: [Char]
- rna_adapter :: [Char]
- rna_adapter2 :: [Char]
- rna_adapter3 :: [Char]
- rapid_adapter :: [Char]
- ti_adapter_b :: [Char]

## Discarding filters

type DiscardFilter = ReadBlock -> Bool

DiscardFilters determine whether a read is to be retained or discarded

discard_empty :: DiscardFilter

This filter discards empty sequences.

discard_key :: String -> DiscardFilter

Discard sequences that don't have the given key tag (typically TCAG) at the start of the read.

discard_dots :: Double -> DiscardFilter

1. 2.2.1.2 The dots filter discards sequences where the last positive flow is before flow 84, and flows with >5% dots (i.e. three successive noise values) before the last postitive flow. The percentage can be given as a parameter.

discard_mixed :: DiscardFilter

1. 2.2.1.3 The mixed filter discards sequences with more than 70% positive flows. Also, discard with noise,20% middle (0.45..0.75) or <30% positive.

discard_length :: Int -> DiscardFilter

Discard a read if the number of untrimmed flows is less than n (n=186 for Titanium)

## Trimming filters

type TrimFilter = ReadBlock -> ReadBlock

TrimFilters modify the read, typically trimming it for quality

trim_sigint :: TrimFilter

1. 2.2.1.4 Signal intensity trim - trim back until <3% borderline flows (0.5..0.7). Then trim borderline values or dots from the end (use a window).

sigint :: ReadBlock -> Int

trim_primer :: String -> TrimFilter

1. 2.2.1.5 Primer filter This looks for the B-adaptor at the end of the read. The 454 implementation isn't very effective at finding mutated adaptors.

find_primer :: String -> ReadBlock -> Int

trim_qual20 :: Int -> TrimFilter

1. 2.2.1.7 Quality score trimming trims using a 10-base window until a Q20 average is found.

qual20 :: Int -> ReadBlock -> Int

## Utility functions

dlength :: [a] -> Double

List length as a double (eliminates many instances of fromIntegral)

avg :: Integral a => [a] -> Double

Calculate average of a list

clipFlows :: ReadBlock -> Int -> ReadBlock

Translate a number of flows to position in sequence, and update clipping data accordingly

clipSeq :: ReadBlock -> Int -> ReadBlock

Update clip_qual_right if more severe than previous value

## Data

flx_linker :: [Char]

ti_linker :: [Char]

rna_adapter :: [Char]

rna_adapter2 :: [Char]

rna_adapter3 :: [Char]

rapid_adapter :: [Char]

ti_adapter_b :: [Char]